MS
HMDB
-The NMDC Schema is a foundational framework designed to standardize metadata for the National Microbiome Data Collaborative (NMDC) and collaborating data providors. By establishing a structured approach to metadata, the NMDC Schema enables researchers to organize, share, and interpret complex datasets with consistency and clarity. The NMDC Schema is critical substrate used to facilitate interoperability and collaboration, as it provide a common language for data exchange across systems and disciplines. In the context of the NMDC, this schema supports the integration of microbiome data from medicine, agriculture, bioenergy, and environmental science into a cohesive platform.
This schema is organized into two modules:
A core set of elements for representing data values represented in LinkML format (https://w3id.org/linkml/) consisting of a set classes, slots, types, and enumerations that are used to define the structure of the NMDC schema.
A subset of the MIxS schema developed by the Genomic Standards Consortium, that is used to describe the environmental context of samples.
URI: https://w3id.org/nmdc/nmdc
"},{"location":"#classes","title":"Classes","text":"Class Description AttributeValue The value for any value of a attribute for a sample ControlledTermValue A controlled term or class from an ontology ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... GeolocationValue A normalized value for a location on the earth's surface ImageValue An attribute value representing an image PersonValue An attribute value representing a person QuantityValue A simple quantity, e TextValue A basic string value TimestampValue A value that is a timestamp CreditAssociation This class supports binding associated researchers to studies Database An abstract holder for any set of metadata and data Doi A centrally registered identifier symbol used to uniquely identify objects gi... EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... FailureCategorization FunctionalAnnotation An assignment of a function term (e FunctionalAnnotationAggMember GenomeFeature A feature localized to an interval along a genome MagBin MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... NamedThing a databased entity or concept/class GeneProduct A molecule encoded by a gene that has an evolved function InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... CalibrationInformation A calibration object that is associated with a process Configuration A set of parameters that define the actions of a process and is shared among ... ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... DataObject An object that primarily consists of symbols that represent information Manifest A qualified collection of DataObjects that can be analyzed together in the sa... MaterialEntity Instrument A material entity that is designed to perform a function in a scientific inve... Sample A sample is a material entity that can be characterized by an experiment Biosample Biological source material which can be characterized by an experiment ProcessedSample Site FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected OntologyClass A representation of class defined in an external ontology ChemicalEntity An atom or molecule that can be represented with a chemical formula EnvironmentalMaterialTerm FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... OrthologyGroup A set of genes or gene products in which all members are orthologous Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... PlannedProcess CollectingBiosamplesFromSite DataGeneration The methods and processes used to generate omics data from a biosample or org... MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... DissolvingProcess A mixing step where a soluble component is mixed with a liquid component Extraction A material separation in which a desired component of an input material is se... FiltrationProcess The process of segregation of phases; e LibraryPreparation MixingProcess The combining of components, particles or layers into a more homogeneous stat... Pooling physical combination of several instances of like material SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... ProtocolExecution A PlannedProces that has PlannedProcess parts StorageProcess A planned process with the objective to preserve and protect material entitie... WorkflowExecution Represents an instance of an execution of a particular workflow MagsAnalysis A workflow execution activity that uses computational binning tools to group ... MetabolomicsAnalysis MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... MetagenomeSequencing Initial sequencing activity that precedes any analysis MetaproteomicsAnalysis MetatranscriptomeAnnotation MetatranscriptomeAssembly MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... NomAnalysis ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... Study A study summarizes the overall goal of a research initiative and outlines the... OntologyRelation A relationship between two ontology classes as specified either directly in t... PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein Protocol"},{"location":"#slots","title":"Slots","text":"Slot Description abs_air_humidity Actual mass of water vapor - mh20 - present in the air water vapor mixture add_date The date on which the information was added to the database add_recov_method Additional (i additional_info Information that doesn't fit anywhere else address The street name and building number where the sampling occurred adj_room List of rooms (room number, room name) immediately adjacent to the sampling r... aero_struc Aerospace structures typically consist of thin plates with stiffeners for the... agrochem_addition Addition of fertilizers, pesticides, etc air_PM_concen Concentration of substances that remain suspended in the air, and comprise mi... air_temp Temperature of the air at the time of sampling air_temp_regm Information about treatment involving an exposure to varying temperatures; sh... al_sat Aluminum saturation (esp al_sat_meth Reference or method used in determining Al saturation alkalinity Alkalinity, the ability of a solution to neutralize acids to the equivalence ... alkalinity_method Method used for alkalinity measurement alkyl_diethers Concentration of alkyl diethers all_proteins the list of protein identifiers that are associated with the peptide sequence alt Altitude is a term used to identify heights of objects such as airplanes, spa... alternative_descriptions A list of alternative descriptions for the entity alternative_identifiers A list of alternative identifiers for the entity alternative_names A list of alternative names used to refer to the entity alternative_titles A list of alternative titles for the entity aminopept_act Measurement of aminopeptidase activity ammonium Concentration of ammonium in the sample ammonium_nitrogen Concentration of ammonium nitrogen in the sample amount_light The unit of illuminance and luminous emittance, measuring luminous flux per u... analysis_identifiers analysis_type Select all the data types associated or available for this biosample analyte_category The type of analyte(s) that were measured in the data generation process and ... ances_data Information about either pedigree or other ancestral information description ... annual_precpt The average of all annual precipitation values known, or an estimated equival... annual_temp Mean annual temperature antibiotic_regm Information about treatment involving antibiotic administration; should inclu... api API gravity is a measure of how heavy or light a petroleum liquid is compared... applied_roles applies_to_person arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c... aromatics_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... asm_score A score for comparing metagenomic assembly quality from same sample asphaltenes_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... assembly_identifiers associated_dois A list of DOIs associated with a resource, such as a list of DOIS associated ... associated_studies The study associated with a resource atmospheric_data Measurement of atmospheric data; can include multiple data avg_dew_point The average of dew point measures taken at the beginning of every hour over a... avg_occup Daily average occupancy of room avg_temp The average of temperatures taken at the beginning of every hour over a 24 ho... bac_prod Bacterial production in the water column measured by isotope uptake bac_resp Measurement of bacterial respiration in the water column bacteria_carb_prod Measurement of bacterial carbon production barometric_press Force per unit area exerted against a surface by the weight of air above that... basin Name of the basin (e bathroom_count The number of bathrooms in the building bedroom_count The number of bedrooms in the building benzene Concentration of benzene in the sample best_protein the specific protein identifier most correctly associated with the peptide se... bin_name Name of the metagenome-assembled genome bin_quality The quality of the metagenome-assembled genome based on MIMAG standards (http... binned_contig_num Number of contigs that ended up in a medium or high quality bin biochem_oxygen_dem Amount of dissolved oxygen needed by aerobic biological organisms in a body o... biocide List of biocides (commercial name of product and supplier) and date of admini... biocide_admin_method Method of biocide administration (dose, frequency, duration, time elapsed bet... biogas_retention_time biogas_temperature biol_stat The level of genome modification biomass Amount of biomass; should include the name for the part of biomass measured, ... biomaterial_purity biosample_categories biosample_identifiers biosample_set This property links a database object to the set of samples within it biotic_regm Information about treatment(s) involving use of biotic factors, such as bacte... biotic_relationship Description of relationship(s) between the subject organism and other organis... bishomohopanol Concentration of bishomohopanol blood_press_diast Resting diastolic blood pressure, measured as mm mercury blood_press_syst Resting systolic blood pressure, measured as mm mercury bromide Concentration of bromide build_docs The building design, construction and operation documents build_occup_type The primary function for which a building or discrete part of a building is i... building_setting A location (geography) where a building is set built_struc_age The age of the built structure since construction built_struc_set The characterization of the location of the built structure as high or low hu... built_struc_type A physical structure that is a body or assemblage of bodies in space to form ... bulk_elect_conductivity Electrical conductivity is a measure of the ability to carry electric current... calcium Concentration of calcium in the sample calibration_object the file containing calibration data object calibration_set This property links a database object to the set of calibrations within it calibration_standard the reference standard(s) used for calibration calibration_target the target measurement of the calibration carb_dioxide Carbon dioxide (gas) amount or concentration at the time of sampling carb_monoxide Carbon monoxide (gas) amount or concentration at the time of sampling carb_nitro_ratio Ratio of amount or concentrations of carbon to nitrogen ceil_area The area of the ceiling space within the room ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide... ceil_finish_mat The type of material used to finish a ceiling ceil_struc The construction format of the ceiling ceil_texture The feel, appearance, or consistency of a ceiling surface ceil_thermal_mass The ability of the ceiling to provide inertia against temperature fluctuation... ceil_type The type of ceiling according to the ceiling's appearance or construction ceil_water_mold Signs of the presence of mold or mildew on the ceiling chem_administration List of chemical compounds administered to the host or site where sampling oc... chem_mutagen Treatment involving use of mutagens; should include the name of mutagen, amou... chem_oxygen_dem A measure of the capacity of water to consume oxygen during the decomposition... chem_treat_method Method of chemical administration(dose, frequency, duration, time elapsed bet... chem_treatment List of chemical compounds administered upstream the sampling location where ... chemical_conversion_category The type of chemical conversion process chemical_entity_set This property links a database object to the set of chemical entities within ... chemical_formula A generic grouping for molecular formulae and empirical formulae chimera_check Tool(s) used for chimera checking, including version number and parameters, t... chloride Concentration of chloride in the sample chlorophyll Concentration of chlorophyll chromatographic_category The type of chromatography used in a process climate_environment Treatment involving an exposure to a particular climate; treatment regimen in... collected_from The Site from which a Biosample was collected collecting_biosamples_from_site_set collection_date The time of sampling, either as an instance (single point in time) or interva... collection_date_inc Date the incubation was harvested/collected/ended collection_time The time of sampling, either as an instance (single point) or interval collection_time_inc Time the incubation was harvested/collected/ended community completeness Estimate of the completeness of the metagenome-assembled genome, estimated by... completion_date compression_type If provided, specifies the compression type concentration The concentration of a substance used in a process conditionings Preliminary treatment of either phase with a suitable solution of the other p... conduc Electrical conductivity of water configuration_set This property links a database object to the set of configurations within it contained_in A type of container container_size The volume of the container an analyte is stored in or an activity takes plac... contamination Estimate of the completeness of the metagenome-assembled genome, estimated by... contig_bp Total size in bp of all contigs contigs The sum of the (length*log(length)) of all contigs, times some constant cool_syst_id The cooling system identifier core_field basic fields count crop_rotation Whether or not crop is rotated, and if yes, rotation schedule ctg_l50 Given a set of contigs, the L50 is defined as the sequence length of the shor... ctg_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... ctg_logsum Maximum contig length ctg_max Maximum contig length ctg_n50 Given a set of contigs, each with its own length, the N50 count is defined as... ctg_n90 Given a set of contigs, each with its own length, the N90 count is defined as... ctg_powsum Powersum of all contigs is the same as logsum except that it uses the sum of ... cult_root_med Name or reference for the hydroponic or in vitro culture rooting medium; can ... cur_land_use Present state of sample site cur_vegetation Vegetation classification from one or more standard classification systems, o... cur_vegetation_meth Reference or method used in vegetation classification data_category The category of the file, such as instrument data from data generation or pro... data_generation_set This property links a database object to the set of data generations within i... data_object_set This property links a database object to the set of data objects within it data_object_type The type of file represented by the data object date_created from database class date_last_rain The date of the last time it rained definition The definition of the ontology term as provided by the ontology density Density of the sample, which is its mass per unit volume (aka volumetric mass... depos_env Main depositional environment (https://en depth The vertical distance below local surface, e description a human-readable description of a thing dew_point The temperature to which a given parcel of humid air must be cooled, at const... diether_lipids Concentration of diether lipids; can include multiple types of diether lipids display_order When rendering information, this attribute to specify the order in which the ... diss_carb_dioxide Concentration of dissolved carbon dioxide in the sample or liquid portion of ... diss_hydrogen Concentration of dissolved hydrogen diss_inorg_carb Dissolved inorganic carbon concentration in the sample, typically measured af... diss_inorg_nitro Concentration of dissolved inorganic nitrogen diss_inorg_phosp Concentration of dissolved inorganic phosphorus in the sample diss_iron Concentration of dissolved iron in the sample diss_org_carb Concentration of dissolved organic carbon in the sample, liquid portion of th... diss_org_nitro Dissolved organic nitrogen concentration measured as; total dissolved nitroge... diss_oxygen Concentration of dissolved oxygen diss_oxygen_fluid Concentration of dissolved oxygen in the oil field produced fluids as it cont... dna_absorb1 260/280 measurement of DNA sample purity dna_absorb2 260/230 measurement of DNA sample purity dna_collect_site Provide information on the site your DNA sample was collected from dna_concentration dna_cont_type Tube or plate (96-well) dna_cont_well dna_container_id dna_dnase dna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA dna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... dna_project_contact dna_samp_id dna_sample_format Solution in which the DNA sample has been suspended dna_sample_name Give the DNA sample a name that is meaningful to you dna_seq_project dna_seq_project_name dna_seq_project_pi dna_volume dnase_rna doi_category The resource type the corresponding doi resolves to doi_provider The authority, or organization, the DOI is associated with doi_value A digital object identifier, which is intended to persistantly identify some ... door_comp_type The composite type of the door door_cond The phsical condition of the door door_direct The direction the door opens door_loc The relative location of the door in the room door_mat The material the door is composed of door_move The type of movement of the door door_size The size of the door door_type The type of door material door_type_metal The type of metal door door_type_wood The type of wood door door_water_mold Signs of the presence of mold or mildew on a door down_par Visible waveband radiance and irradiance measurements in the water column drainage_class Drainage classification from a standard system such as the USDA system drawings The buildings architectural drawings; if design is chosen, indicate phase-con... duration The elapsed time of an activity ecosystem An ecosystem is a combination of a physical environment (abiotic factors) and... ecosystem_category Ecosystem categories represent divisions within the ecosystem based on specif... ecosystem_path_id A unique id representing the GOLD classifiers associated with a sample ecosystem_subtype Ecosystem subtypes represent further subdivision of Ecosystem types into more... ecosystem_type Ecosystem types represent things having common characteristics within the Eco... efficiency_percent Percentage of volatile solids removed from the anaerobic digestor elev Elevation of the sampling site is its height above a fixed reference point, m... elevator The number of elevators within the built structure eluent_introduction_category A high-level categorization for how the processed sample is introduced into a... email An email address for an entity such as a person embargoed If true, the data are embargoed and not available for public access emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database emsl_identifiers emsl_project_identifiers Identifiers that link a NMDC study to the EMSL user facility website hosting ... emsl_store_temp The temperature at which the sample should be stored upon delivery to EMSL emulsions Amount or concentration of substances such as paints, adhesives, mayonnaise, ... encodes The gene product encoded by this feature end The end of the feature in positive 1-based integer coordinates end_date The date on which any process or activity was ended ended_at_time env_broad_scale Report the major environmental system the sample or specimen came from env_local_scale Report the entity or entities which are in the sample or specimen\u2019s local vic... env_medium Report the environmental material(s) immediately surrounding the sample or sp... env_package MIxS extension for reporting of measurements and observations obtained from o... environment_field field describing environmental aspect of a sample escalator The number of escalators within the built structure ethylbenzene Concentration of ethylbenzene in the sample etl_software_version from database class eukaryotic_evaluation Contains results from evaluating if a Metagenome-Assembled Genome is of eukar... execution_resource The computing resource or facility where the workflow was executed exp_duct The amount of exposed ductwork in the room exp_pipe The number of exposed pipes in the room experimental_factor Experimental factors are essentially the variable aspects of an experiment de... experimental_factor_other Other details about your sample that you feel can't be accurately represented... ext_door The number of exterior doors in the built structure ext_wall_orient The orientation of the exterior wall ext_window_orient The compass direction the exterior window of the room is facing external_database_identifiers Link to corresponding identifier in external database extraction_targets Provides the target biomolecule that has been separated from a sample during ... extreme_event Unusual physical events that may have affected microbial populations fao_class Soil classification from the FAO World Reference Database for Soil Resources feature_category A Sequence Ontology term that describes the category of a feature feature_type TODO: Yuri to write fertilizer_regm Information about treatment involving the use of fertilizers; should include ... field Name of the hydrocarbon field (e field_research_site_set file_size_bytes Size of the file in bytes filter_material A porous material on which solid particles present in air or other fluid whic... filter_method Type of filter used or how the sample was filtered filter_pore_size A quantitative or qualitative measurement of the physical dimensions of the p... filter_type A device which removes solid particulates or airborne molecular contaminants filtration_category The type of conditioning applied to a filter, device, etc final_concentration When solutions A (containing substance X) and B are combined together, this s... fire Historical and/or physical evidence of fire fireplace_type A firebox with chimney flooding Historical and/or physical evidence of flooding floor_age The time period since installment of the carpet or flooring floor_area The area of the floor space within the room floor_cond The physical condition of the floor at the time of sampling; photos or video ... floor_count The number of floors in the building, including basements and mechanical pent... floor_finish_mat The floor covering type; the finished surface that is walked on floor_struc Refers to the structural elements and subfloor upon which the finish flooring... floor_thermal_mass The ability of the floor to provide inertia against temperature fluctuations floor_water_mold Signs of the presence of mold or mildew in a room fluor Raw or converted fluorescence of water freq_clean The number of times the sample location is cleaned freq_cook The number of times a meal is cooked per week functional_annotation_agg functional_annotation_set This property links a database object to the set of all functional annotation... funding_sources A list of organizations, along with the award numbers, that underwrite financ... fungicide_regm Information about treatment involving use of fungicides; should include the n... furniture The types of furniture present in the sampled room gap_pct The gap size percentage of all scaffolds gaseous_environment Use of conditions with differing gaseous environments; should include the nam... gaseous_substances Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... gc_avg Average of GC content of all contigs gc_std Standard deviation of GC content of all contigs gender_restroom The gender type of the restroom gene_count Number of genes gene_function_id The identifier for the gene function generates_calibration calibration information is generated a process genetic_mod Genetic modifications of the genome of an organism, which may occur naturally... genome_feature_set This property links a database object to the set of all features geo_loc_name The geographical origin of the sample as defined by the country or sea name f... gff_coordinate A positive 1-based integer coordinate indicating start or end git_url The url that points to the exact github location of a workflow glucosidase_act Measurement of glucosidase activity gnps_identifiers gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... gold_analysis_project_identifiers identifiers for corresponding analysis projects in GOLD gold_biosample_identifiers identifiers for corresponding sample in GOLD gold_identifiers gold_path_field This is a grouping for any of the gold path fields gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD gold_study_identifiers identifiers for corresponding project(s) in GOLD gravidity Whether or not subject is gravid, and if yes date due or date post-conception... gravity Information about treatment involving use of gravity factor to study various ... growth_facil Type of facility where the sampled plant was grown; controlled vocabulary: gr... growth_habit Characteristic shape, appearance or growth form of a plant species growth_hormone_regm Information about treatment involving use of growth hormones; should include ... gtdbtk_class Taxonomic class assigned by GTDB-Tk gtdbtk_domain Taxonomic domain assigned by GTDB-Tk gtdbtk_family Taxonomic family assigned by GTDB-Tk gtdbtk_genus Taxonomic genus assigned by GTDB-Tk gtdbtk_order Taxonomic order assigned by GTDB-Tk gtdbtk_phylum Taxonomic phylum assigned by GTDB-Tk gtdbtk_species Taxonomic genus assigned by GTDB-Tk habitat hall_count The total count of hallways and cooridors in the built structure handidness The handidness of the individual sampled has_boolean_value Links a quantity value to a boolean has_chromatography_configuration The identifier of the associated ChromatographyConfiguration, providing infor... has_credit_associations This slot links a study to a credit association has_failure_categorization has_function has_input An input to a process has_mass_spectrometry_configuration The identifier of the associated MassSpectrometryConfiguration has_maximum_numeric_value The maximum value part, expressed as number, of the quantity value when the v... has_metabolite_identifications has_minimum_numeric_value The minimum value part, expressed as number, of the quantity value when the v... has_numeric_value Links a quantity value to a number has_output An output from a process has_peptide_quantifications has_process_parts A list of process parts that make up a protocol has_raw_value The value that was specified for an annotation in raw form, i has_unit Links a QuantityValue to a unit hc_produced Main hydrocarbon type produced from resource (i hcr Main Hydrocarbon Resource type hcr_fw_salinity Original formation water salinity (prior to secondary recovery e hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en hcr_pressure Original pressure of the hydrocarbon resource hcr_temp Original temperature of the hydrocarbon resource heat_cool_type Methods of conditioning or heating a room or building heat_deliv_loc The location of heat delivery within the room heat_sys_deliv_meth The method by which the heat is delivered through the system heat_system_id The heating system identifier heavy_metals Heavy metals present in the sequenced sample and their concentrations heavy_metals_meth Reference or method used in determining heavy metals height_carper_fiber The average carpet fiber height in the indoor environment herbicide_regm Information about treatment involving use of herbicides; information about tr... highest_similarity_score homepage_website The website address (URL) of an entity's homepage horizon_meth Reference or method used in determining the horizon host_age Age of host at the time of sampling; relevant scale depends on species and st... host_body_habitat Original body habitat where the sample was obtained from host_body_product Substance produced by the body, e host_body_site Name of body site where the sample was obtained from, such as a specific orga... host_body_temp Core body temperature of the host when sample was collected host_color The color of host host_common_name Common name of the host host_diet Type of diet depending on the host, for animals omnivore, herbivore etc host_disease_stat List of diseases with which the host has been diagnosed; can include multiple... host_dry_mass Measurement of dry mass host_family_relation Familial relationships to other hosts in the same study; can include multiple... host_genotype Observed genotype host_growth_cond Literature reference giving growth conditions of the host host_height The height of subject host_last_meal Content of last meal and time since feeding; can include multiple values host_length The length of subject host_life_stage Description of life stage of host host_name host_phenotype Phenotype of human or other host host_sex Gender or physical sex of the host host_shape Morphological shape of host host_subject_id A unique identifier by which each subject can be referred to, de-identified host_subspecf_genlin Information about the genetic distinctness of the host organism below the sub... host_substrate The growth substrate of the host host_symbiont The taxonomic name of the organism(s) found living in mutualistic, commensali... host_taxid NCBI taxon id of the host, e host_tot_mass Total mass of the host at collection, the unit depends on host host_wet_mass Measurement of wet mass humidity Amount of water vapour in the air, at the time of sampling humidity_regm Information about treatment involving an exposure to varying degree of humidi... id A unique identifier for a thing igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database igsn_identifiers img_identifiers A list of identifiers that relate the biosample to records in the IMG databas... in_manifest one or more combinations of other DataObjects that can be analyzed together inchi inchi_key indoor_space A distinguishable space within a structure, the purpose for which discrete ar... indoor_surf Type of indoor surface indust_eff_percent Percentage of industrial effluents received by wastewater treatment plant infiltrations The amount of time it takes to complete each infiltration activity inorg_particles Concentration of particles such as sand, grit, metal particles, ceramics, etc input_base_count The nucleotide base count number of input reads for QC analysis input_contig_num Total number of input contigs input_mass Total mass of sample used in activity input_read_bases TODO input_read_count The sequence count number of input reads for QC analysis input_volume The volume of the input sample insdc_analysis_identifiers insdc_assembly_identifiers insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject insdc_biosample_identifiers identifiers for corresponding sample in INSDC insdc_experiment_identifiers insdc_identifiers Any identifier covered by the International Nucleotide Sequence Database Coll... insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA inside_lux The recorded value at sampling time (power density) instrument_set This property links a database object to the set of instruments within it instrument_used What instrument was used during DataGeneration or MaterialProcessing int_wall_cond The physical condition of the wall at the time of sampling; photos or video p... internal_calibration whether internal calibration was used, if false, external calibration was use... investigation_field field describing aspect of the investigation/study to which the sample belong... ionization_source The ionization source used to introduce processed samples into a mass spectro... is_pressurized Whether or not pressure was applied to a thing or process is_stranded Is the (RNA) library stranded or non-stranded (unstranded) isotope_exposure List isotope exposure or addition applied to your sample iw_bt_date_well Injection water breakthrough date per well following a secondary and/or terti... iwf Proportion of the produced fluids derived from injected water at the time of ... jgi_portal_analysis_project_identifiers identifiers for corresponding analysis projects in JGI Portal jgi_portal_identifiers identifiers for entities according to JGI Portal jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... known_as The substance from which a portion was taken language Should use ISO 639-1 code e last_clean The last time the floor was cleaned (swept, mopped, vacuumed) lat_lon The geographical origin of the sample as defined by latitude and longitude latitude latitude lbc_thirty lime buffer capacity, determined after 30 minute incubation lbceq lime buffer capacity, determined at equilibrium after 5 day incubation library_preparation_kit library_type light_intensity Measurement of light intensity light_regm Information about treatment(s) involving exposure to light, including both li... light_type Application of light to achieve some practical or aesthetic effect link_addit_analys Link to additional analysis results performed on the sample link_class_info Link to digitized soil maps or other soil classification information link_climate_info Link to climate resource lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki local_class Soil classification based on local soil classification system local_class_meth Reference or method used in determining the local soil classification location longitude longitude low_depth_contig_num Number of contigs which were excluded from binning for depth of coverage magnesium Concentration of magnesium in the sample mags_list Contains detailed information about each metagenome-assembled genome manganese Concentration of manganese in the sample manifest_category The type of context in which the constituent DataObjects can be analyzed toge... manifest_set This property links a database object to the set of manifests within it mass A physical quality that inheres in a bearer by virtue of the proportion of th... mass_analyzers The kind of mass analyzer(s) used during the spectra collection mass_spectrometry_acquisition_strategy Mode of running a mass spectrometer method by which m/z ranges are selected a... mass_spectrum_collection_modes Indicates whether mass spectra were collected in full profile, reduced profil... material_component_separation A material processing in which components of an input material become segrega... material_processing_set This property links a database object to the set of material processing withi... max_occup The maximum amount of people allowed in the indoor environment md5_checksum MD5 checksum of file (pre-compressed) mean_frict_vel Measurement of mean friction velocity mean_peak_frict_vel Measurement of mean peak friction velocity mech_struc mechanical structure: a moving structure mechanical_damage Information about any mechanical damage exerted on the plant; can include mul... members_id Names of the contigs that make up a metagenome-assembled genome metabolite_identified the specific metabolite identifier metagenome_annotation_id The identifier for the analysis activity that generated the functional annota... metagenome_assembly_parameter metaproteomics_analysis_category The category of metaproteomics analysis being performed methane Methane (gas) amount or concentration at the time of sampling mgnify_analysis_identifiers mgnify_identifiers mgnify_project_identifiers identifiers for corresponding project in MGnify micro_biomass_c_meth Reference or method used in determining microbial biomass carbon micro_biomass_meth Reference or method used in determining microbial biomass micro_biomass_n_meth Reference or method used in determining microbial biomass nitrogen microbial_biomass The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_c The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_n The part of the organic matter in the soil that constitutes living microorgan... min_q_value smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... mineral_nutr_regm Information about treatment involving the use of mineral supplements; should ... misc_param Any other measurement performed or parameter collected, that is not listed he... mod_date The last date on which the database information was modified model modifier_substance The type of modification being done n_alkanes Concentration of n-alkanes; can include multiple n-alkanes name A human readable label for an entity ncbi_lineage Comma delimited ordered list of NCBI taxonomy names ncbi_lineage_tax_ids Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId) ncbi_project_name ncbi_taxonomy_name neon_biosample_identifiers neon_identifiers identifiers for entities according to NEON neon_study_identifiers nitrate Concentration of nitrate in the sample nitrate_nitrogen Concentration of nitrate nitrogen in the sample nitrite Concentration of nitrite in the sample nitrite_nitrogen Concentration of nitrite nitrogen in the sample nitro Concentration of nitrogen (total) non_microb_biomass Amount of biomass; should include the name for the part of biomass measured, ... non_microb_biomass_method Reference or method used in determining biomass non_min_nutr_regm Information about treatment involving the exposure of plant to non-mineral nu... notes nucl_acid_amp A link to a literature reference, electronic resource or a standard operating... nucl_acid_ext A link to a literature reference, electronic resource or a standard operating... nucleic_acid_sequence_source_field num_16s Number of 16s sequences detected, a subunit of prokaryotic ribosomes num_23s Number of 23 seqeuences detected, a subunit of ribosomes num_5s Number of 5s seqeuences detected, a subunit of ribosomes num_aligned_reads The sequence count number of input reads aligned to assembled contigs num_input_reads The sequence count number of input reads for assembly num_t_rna Number of transfer transfer RNAs number_of_contig Number of contigs number_pets The number of pets residing in the sampled space number_plants The number of plant(s) in the sampling space number_resident The number of individuals currently occupying in the sampling location object object_set Applies to a property that links a database object to a set of objects objective The scientific objectives associated with the entity occup_density_samp Average number of occupants at time of sampling per square footage occup_document The type of documentation of occupancy occup_samp Number of occupants present at time of sample within the given space omics_processing_identifiers omics_type The type of omics data ontology_class_set This property links a database object to the set of ontology classes within i... orcid The ORCID of a person ordered_mobile_phases The solution(s) that moves through a chromatography column org_carb Concentration of organic carbon org_count_qpcr_info If qpcr was used for the cell count, the target gene name, the primer sequenc... org_matter Concentration of organic matter org_nitro Concentration of organic nitrogen org_nitro_method Method used for obtaining organic nitrogen org_particles Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... organism_count Total cell count of any organism (or group of organisms) per gram, volume or ... other_treatment Other treatments applied to your samples that are not applicable to the provi... output_base_count After QC analysis nucleotide base count number output_read_bases TODO output_read_count After QC analysis sequence count number owc_tvdss Depth of the original oil water contact (OWC) zone (average) (m TVDSS) oxy_stat_samp Oxygenation status of sample oxygen Oxygen (gas) amount or concentration at the time of sampling part_of Links a resource to another resource that either logically or physically incl... part_org_carb Concentration of particulate organic carbon part_org_nitro Concentration of particulate organic nitrogen particle_class Particles are classified, based on their size, into six general categories:cl... pcr_cond Description of reaction conditions and components of PCR in the form of 'init... pcr_cycles pcr_primers PCR primers that were used to amplify the sequence of the targeted gene, locu... peptide_sequence peptide_sequence_count count of peptide sequences grouped to the best_protein peptide_spectral_count sum of filter passing MS2 spectra associated with the peptide sequence within... peptide_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... permeability Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... perturbation Type of perturbation, e pesticide_regm Information about treatment involving use of insecticides; should include the... petroleum_hydrocarb Concentration of petroleum hydrocarbon ph Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... ph_meth Reference or method used in determining ph ph_regm Information about treatment involving exposure of plants to varying levels of... phaeopigments Concentration of phaeopigments; can include multiple phaeopigments phase The phase for a coding sequence entity phosphate Concentration of phosphate phosplipid_fatt_acid Concentration of phospholipid fatty acids; can include multiple values photon_flux Measurement of photon flux plant_growth_med Specification of the media for growing the plants or tissue cultured samples,... plant_product Substance produced by the plant, where the sample was obtained from plant_sex Sex of the reproductive parts on the whole plant, e plant_struc Name of plant structure the sample was obtained from; for Plant Ontology (PO)... polarity_mode the polarity of which ions are generated and detected pollutants Pollutant types and, amount or concentrations measured at the time of samplin... pool_dna_extracts Indicate whether multiple DNA extractions were mixed porosity Porosity of deposited sediment is volume of voids divided by the total volume... potassium Concentration of potassium in the sample pour_point Temperature at which a liquid becomes semi solid and loses its flow character... pre_treatment The process of pre-treatment removes materials that can be easily collected f... predicate pres_animal_insect The type and number of animals or insects present in the sampling space pressure Pressure to which the sample is subject to, in atmospheres prev_land_use_meth Reference or method used in determining previous land use and dates previous_land_use Previous land use and dates primary_prod Measurement of primary production, generally measured as isotope uptake primary_treatment The process to produce both a generally homogeneous liquid capable of being t... principal_investigator Principal Investigator who led the study and/or generated the dataset processed_sample_set This property links a database object to the set of processed samples within ... processing_institution The organization that processed the sample prod_rate Oil and/or gas production rates per well (e prod_start_date Date of field's first production profile_image_url A url that points to an image of a person profile_position Cross-sectional position in the hillslope where sample was collected project_id Proposal IDs or names associated with dataset proport_woa_temperature proposal_dna proposal_rna protein_spectral_count sum of filter passing MS2 spectra associated with the best protein within a g... protein_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... protocol_execution_category protocol_execution_set This property links a database object to the set of protocol executions withi... protocol_link qc_comment Slot to store additional comments about laboratory or workflow output qc_failure_what Provides a summary about what caused a lab or workflow process to fail qc_failure_where Describes the nmdc schema class that corresonds to where the failure occurred qc_status Stores information about the result of a process (ie the process of sequencin... quad_pos The quadrant position of the sampling room within the building radiation_regm Information about treatment involving exposure of plant or a plant part to a ... rainfall_regm Information about treatment involving an exposure to a given amount of rainfa... reactor_type Anaerobic digesters can be designed and engineered to operate using a number ... read_qc_analysis_statistic redox_potential Redox potential, measured relative to a hydrogen cell, indicating oxidation o... rel_air_humidity Partial vapor and air pressure, density of the vapor and air, or by the actua... rel_humidity_out The recorded outside relative humidity value at the time of sampling rel_samp_loc The sampling location within the train car related_identifiers Identifiers assigned to a thing that is similar to that which is represented ... relations replicate_number If sending biological replicates, indicate the rep number here reservoir Name of the reservoir (e resins_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... resolution_categories The relative resolution at which spectra were collected rna_absorb1 260/280 measurement of RNA sample purity rna_absorb2 260/230 measurement of RNA sample purity rna_collect_site Provide information on the site your RNA sample was collected from rna_concentration rna_cont_type Tube or plate (96-well) rna_cont_well rna_container_id rna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA rna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... rna_project_contact rna_samp_id rna_sample_format Solution in which the RNA sample has been suspended rna_sample_name Give the RNA sample a name that is meaningful to you rna_seq_project rna_seq_project_name rna_seq_project_pi rna_volume room_air_exch_rate The rate at which outside air replaces indoor air in a given space room_architec_elem The unique details and component parts that, together, form the architecture ... room_condt The condition of the room at the time of sampling room_connected List of rooms connected to the sampling room by a doorway room_count The total count of rooms in the built structure including all room types room_dim The length, width and height of sampling room room_door_dist Distance between doors (meters) in the hallway between the sampling room and ... room_door_share List of room(s) (room number, room name) sharing a door with the sampling roo... room_hallway List of room(s) (room number, room name) located in the same hallway as sampl... room_loc The position of the room within the building room_moist_dam_hist The history of moisture damage or mold in the past 12 months room_net_area The net floor area of sampling room room_occup Count of room occupancy at time of sampling room_samp_pos The horizontal sampling position in the room relative to architectural elemen... room_type The main purpose or activity of the sampling room room_vol Volume of sampling room room_wall_share List of room(s) (room number, room name) sharing a wall with the sampling roo... room_window_count Number of windows in the room root_cond Relevant rooting conditions such as field plot size, sowing density, containe... root_med_carbon Source of organic carbon in the culture rooting medium; e root_med_macronutr Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... root_med_micronutr Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... root_med_ph pH measurement of the culture rooting medium; e root_med_regl Growth regulators in the culture rooting medium such as cytokinins, auxins, g... root_med_solid Specification of the solidifying agent in the culture rooting medium; e root_med_suppl Organic supplements of the culture rooting medium, such as vitamins, amino ac... salinity The total concentration of all dissolved salts in a liquid or solid sample salinity_category Categorical description of the sample's salinity salinity_meth Reference or method used in determining salinity salt_regm Information about treatment involving use of salts as supplement to liquid an... samp_capt_status Reason for the sample samp_collec_device The device used to collect an environmental sample samp_collec_method The method employed for collecting the sample samp_collect_point Sampling point on the asset were sample was collected (e samp_dis_stage Stage of the disease at the time of sample collection, e samp_floor The floor of the building, where the sampling room is located samp_loc_corr_rate Metal corrosion rate is the speed of metal deterioration due to environmental... samp_mat_process A brief description of any processing applied to the sample during or after r... samp_md In non deviated well, measured depth is equal to the true vertical depth, TVD... samp_name A local identifier or name that for the material sample used for extracting n... samp_preserv Preservative added to the sample (e samp_room_id Sampling room number samp_size The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... samp_sort_meth Method by which samples are sorted; open face filter collecting total suspend... samp_store_dur Duration for which the sample was stored samp_store_loc Location at which sample was stored, usually name of a specific freezer/room samp_store_temp Temperature at which sample was stored, e samp_subtype Name of sample sub-type samp_taxon_id NCBI taxon id of the sample samp_time_out The recent and long term history of outside sampling samp_transport_cond Sample transport duration (in days or hrs) and temperature the sample was exp... samp_tvdss Depth of the sample i samp_type The type of material from which the sample was obtained samp_vol_we_dna_ext Volume (ml) or mass (g) of total collected sample processed for DNA extractio... samp_weather The weather on the sampling day samp_well_name Name of the well (e sample_collection_day sample_collection_hour sample_collection_minute sample_collection_month sample_collection_site sample_collection_year sample_link A unique identifier to assign parent-child, subsample, or sibling samples sample_shipped The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... sample_state_information The chemical phase of a pure sample, or the state of a mixed sample sample_type Type of sample being submitted sampled_portion The portion of the sample that is taken for downstream activity saturates_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... scaf_bp Total size in bp of all scaffolds scaf_l50 Given a set of scaffolds, the L50 is defined as the sequence length of the sh... scaf_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... scaf_l_gt50k Total size in bp of all scaffolds greater than 50 KB scaf_logsum The sum of the (length*log(length)) of all scaffolds, times some constant scaf_max Maximum scaffold length scaf_n50 Given a set of scaffolds, each with its own length, the N50 count is defined ... scaf_n90 Given a set of scaffolds, each with its own length, the N90 count is defined ... scaf_n_gt50k Total sequence count of scaffolds greater than 50 KB scaf_pct_gt50k Total sequence size percentage of scaffolds greater than 50 KB scaf_powsum Powersum of all scaffolds is the same as logsum except that it uses the sum o... scaffolds Total sequence count of all scaffolds season The season when sampling occurred season_environment Treatment involving an exposure to a particular season (e season_precpt The average of all seasonal precipitation values known, or an estimated equiv... season_temp Mean seasonal temperature season_use The seasons the space is occupied secondary_treatment The process for substantially degrading the biological content of the sewage sediment_type Information about the sediment type based on major constituents separation_method The method that was used to separate a substance from a solution or mixture seq_meth Sequencing machine used seq_quality_check Indicate if the sequence has been called by automatic systems (none) or under... seqid The ID of the landmark used to establish the coordinate system for the curren... sequencing_field sewage_type Type of wastewater treatment plant as municipial or industrial shad_dev_water_mold Signs of the presence of mold or mildew on the shading device shading_device_cond The physical condition of the shading device at the time of sampling shading_device_loc The location of the shading device in relation to the built structure shading_device_mat The material the shading device is composed of shading_device_type The type of shading device sieving Collection design of pooled samples and/or sieve size and amount of sample si... silicate Concentration of silicate size_frac Filtering pore size used in sample preparation size_frac_low Refers to the mesh/pore size used to pre-filter/pre-sort the sample size_frac_up Refers to the mesh/pore size used to retain the sample slope_aspect The direction a slope faces slope_gradient Commonly called 'slope' sludge_retent_time The time activated sludge remains in reactor smiles A string encoding of a molecular graph, no chiral or isotopic information sodium Sodium concentration in the sample soil_annual_season_temp soil_horizon Specific layer in the land area which measures parallel to the soil surface a... soil_text_measure The relative proportion of different grain sizes of mineral particles in a so... soil_texture_meth Reference or method used in determining soil texture soil_type Description of the soil type or classification soil_type_meth Reference or method used in determining soil series name or other lower-level... solar_irradiance The amount of solar energy that arrives at a specific area of a surface durin... soluble_inorg_mat Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... soluble_iron_micromol soluble_org_mat Concentration of substances such as urea, fruit sugars, soluble proteins, dru... soluble_react_phosp Concentration of soluble reactive phosphorus source_concentration When solutions A (containing substance X) and B are combined together, this s... source_mat_id A unique identifier assigned to a material sample (as defined by http://rs space_typ_state Customary or normal state of the space specific The building specifications specific_ecosystem Specific ecosystems represent specific features of the environment like aphot... specific_humidity The mass of water vapour in a unit mass of moist air, usually expressed as gr... sr_dep_env Source rock depositional environment (https://en sr_geol_age Geological age of source rock (Additional info: https://en sr_kerog_type Origin of kerogen sr_lithology Lithology of source rock (https://en standing_water_regm Treatment involving an exposure to standing water during a plant's life span,... start The start of the feature in positive 1-based integer coordinates start_date The date on which any process or activity was started start_date_inc Date the incubation was started start_time_inc Time the incubation was started started_at_time stationary_phase The material the stationary phase is comprised of used in chromatography storage_process_set This property links a database object to the set of storage processes within ... store_cond Explain how and for how long the soil sample was stored before DNA extraction... strand The strand on which a feature is located stranded_orientation Lists the strand orientiation for a stranded RNA library preparation study_category The type of research initiative study_identifiers study_image Links a study to one or more images study_set This property links a database object to the set of studies within it subject substance_role The role of a substance in a process substances_used The substances that are combined to enable a ChemicalConversionProcess substances_volume The volume of the combined substances that was included in a ChemicalConversi... substructure_type The substructure or under building is that largely hidden section of the buil... subsurface_depth sulfate Concentration of sulfate in the sample sulfate_fw Original sulfate concentration in the hydrocarbon resource sulfide Concentration of sulfide in the sample surf_air_cont Contaminant identified on surface surf_humidity Surfaces: water activity as a function of air and material moisture surf_material Surface materials at the point of sampling surf_moisture Water held on a surface surf_moisture_ph ph measurement of surface surf_temp Temperature of the surface at the time of sampling suspend_part_matter Concentration of suspended particulate matter suspend_solids Concentration of substances including a wide variety of material, such as sil... tan Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by th... target_gene Targeted gene or locus name for marker gene studies target_subfragment Name of subfragment of a gene or locus technical_reps If sending technical replicates of the same sample, indicate the replicate co... temp Temperature of the sample at the time of sampling temp_out The recorded temperature value at sampling time outside temperature The value of a temperature measurement or temperature used in a process term pointer to an ontology class tertiary_treatment The process providing a final treatment stage to raise the effluent quality b... tidal_stage Stage of tide tillage Note method(s) used for tilling tiss_cult_growth_med Description of plant tissue culture growth media used title A name given to the entity that differs from the name/label programmatically ... toluene Concentration of toluene in the sample too_short_contig_num Number of contigs which were excluded from binning for length tot_carb Total carbon content tot_depth_water_col Measurement of total depth of water column tot_diss_nitro Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... tot_inorg_nitro Total inorganic nitrogen content tot_iron Concentration of total iron in the sample tot_nitro Total nitrogen concentration of water samples, calculated by: total nitrogen ... tot_nitro_cont_meth Reference or method used in determining the total nitrogen tot_nitro_content Total nitrogen content of the sample tot_org_c_meth Reference or method used in determining total organic carbon tot_org_carb Definition for soil: total organic carbon content of the soil, definition oth... tot_part_carb Total particulate carbon content tot_phosp Total phosphorus concentration in the sample, calculated by: total phosphorus... tot_phosphate Total amount or concentration of phosphate tot_sulfur Concentration of total sulfur in the sample total_bases Total number of basepairs train_line The subway line name train_stat_loc The train station collection location train_stop_loc The train stop collection location turbidity Measure of the amount of cloudiness or haziness in water caused by individual... tvdss_of_hcr_press True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... tvdss_of_hcr_temp True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... typ_occup_density Customary or normal density of occupants type the class_uri of the class that has been instantiated unbinned_contig_num Number of contigs which did not end up in a medium or high quality bin url uses_calibration calibration information is used by a process value vendor ventilation_rate Ventilation rate of the system in the sampled premises ventilation_type Ventilation system used in the sampled premises version vfa Concentration of Volatile Fatty Acids in the sample vfa_fw Original volatile fatty acid concentration in the hydrocarbon resource vis_media The building visual media viscosity A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020t... volatile_org_comp Concentration of carbon-based chemicals that easily evaporate at room tempera... volume The volume of a substance wall_area The total area of the sampled room's walls wall_const_type The building class of the wall defined by the composition of the building ele... wall_finish_mat The material utilized to finish the outer most layer of the wall wall_height The average height of the walls in the sampled room wall_loc The relative location of the wall within the room wall_surf_treatment The surface treatment of interior wall wall_texture The feel, appearance, or consistency of a wall surface wall_thermal_mass The ability of the wall to provide inertia against temperature fluctuations wall_water_mold Signs of the presence of mold or mildew on a wall was_generated_by was_informed_by wastewater_type The origin of wastewater such as human waste, rainfall, storm drains, etc water_cont_soil_meth Reference or method used in determining the water content of soil water_content Water content measurement water_current Measurement of magnitude and direction of flow within a fluid water_cut Current amount of water (%) in a produced fluid stream; or the average of the... water_feat_size The size of the water feature water_feat_type The type of water feature present within the building being sampled water_prod_rate Water production rates per well (e water_temp_regm Information about treatment involving an exposure to water with varying degre... watering_regm Information about treatment involving an exposure to watering frequencies, tr... websites A list of websites that are associated with the entity weekday The day of the week when sampling occurred win A unique identifier of a well or wellbore wind_direction Wind direction is the direction from which a wind originates wind_speed Speed of wind measured at the time of sampling window_cond The physical condition of the window at the time of sampling window_cover The type of window covering window_horiz_pos The horizontal position of the window on the wall window_loc The relative location of the window within the room window_mat The type of material used to finish a window window_open_freq The number of times windows are opened per week window_size The window's length and width window_status Defines whether the windows were open or closed during environmental testing window_type The type of windows window_vert_pos The vertical position of the window on the wall window_water_mold Signs of the presence of mold or mildew on the window workflow_execution_set This property links a database object to the set of workflow executions xylene Concentration of xylene in the sample zinc Concentration of zinc in the sample"},{"location":"#enumerations","title":"Enumerations","text":"Enumeration Description AnalysisTypeEnum ArchStrucEnum BinQualityEnum BiolStatEnum BiosampleCategoryEnum Funding-based, sample location-based, or experimental method-based defined ca... BioticRelationshipEnum BuildDocsEnum BuildOccupTypeEnum BuildingSettingEnum CalibrationStandardEnum CalibrationTargetEnum CeilCondEnum CeilFinishMatEnum CeilTextureEnum CeilTypeEnum ChemicalConversionCategoryEnum ChemicalEntityEnum ChromatographicCategoryEnum ContainerCategoryEnum The permitted types of containers used in processing metabolomic samples CreditEnum CurLandUseEnum DataCategoryEnum DeposEnvEnum DNASampleFormatEnum DoiCategoryEnum DoiProviderEnum DoorCompTypeEnum DoorCondEnum DoorDirectEnum DoorLocEnum DoorMatEnum DoorMoveEnum DoorTypeEnum DoorTypeMetalEnum DoorTypeWoodEnum DrainageClassEnum DrawingsEnum EluentIntroductionCategoryEnum ExecutionResourceEnum ExtWallOrientEnum ExtWindowOrientEnum ExtractionTargetEnum FailureWhatEnum The permitted values for describing where a failure occurred during processin... FailureWhereEnum The permitted values for describing where in the process, either a lab or ana... FaoClassEnum FileTypeEnum FilterTypeEnum FloorCondEnum FloorFinishMatEnum FloorStrucEnum FloorWaterMoldEnum FreqCleanEnum FurnitureEnum GenderRestroomEnum GrowthHabitEnum HandidnessEnum HcProducedEnum HcrEnum HcrGeolAgeEnum HeatCoolTypeEnum HeatDelivLocEnum HostSexEnum IndoorSpaceEnum IndoorSurfEnum InstrumentModelEnum InstrumentVendorEnum IntWallCondEnum IonizationSourceEnum JgiContTypeEnum LibraryTypeEnum LightTypeEnum LithologyEnum ManifestCategoryEnum A list of contexts in which some DataObjects can be analyzed together MassAnalyzerEnum MassSpectrometryAcquisitionStrategyEnum MassSpectrometryEnum MassSpectrumCollectionModeEnum MechStrucEnum MetaproteomicsAnalysisCategoryEnum The category of metaproteomics analysis being performed NucleotideSequencingEnum OccupDocumentEnum OrganismCountEnum OxyStatSampEnum PlantGrowthMedEnum PlantSexEnum PolarityModeEnum ProcessingInstitutionEnum ProfilePositionEnum ProtocolCategoryEnum The possible protocols that may be followed for an assay QuadPosEnum RelSampLocEnum ResolutionCategoryEnum RNASampleFormatEnum RoomCondtEnum RoomConnectedEnum RoomLocEnum RoomSampPosEnum RoomTypeEnum SampCaptStatusEnum SampCollectPointEnum SampDisStageEnum SampFloorEnum SampMdEnum SampSubtypeEnum SampWeatherEnum SamplePortionEnum SampleStateEnum SampleTypeEnum SeasonUseEnum SedimentTypeEnum SeparationMethodEnum The tool/substance used to separate or filter a solution or mixture ShadingDeviceCondEnum ShadingDeviceTypeEnum SoilHorizonEnum SpecificEnum SrDepEnvEnum SrGeolAgeEnum SrKerogTypeEnum SrLithologyEnum StationaryPhaseEnum The type of stationary phase used in a chromatography process StatusEnum StrandedOrientationEnum This enumeration specifies information about stranded RNA library preparation... StudyCategoryEnum SubstanceRoleEnum SubstructureTypeEnum SurfAirContEnum SurfMaterialEnum TargetGeneEnum TidalStageEnum TillageEnum TrainLineEnum TrainStatLocEnum TrainStopLocEnum VisMediaEnum WallConstTypeEnum WallFinishMatEnum WallLocEnum WallSurfTreatmentEnum WallTextureEnum WaterFeatTypeEnum WeekdayEnum WindowCondEnum WindowCoverEnum WindowHorizPosEnum WindowLocEnum WindowMatEnum WindowTypeEnum WindowVertPosEnum YesNoEnum replaces DnaDnaseEnum and DnaseRnaEnum"},{"location":"#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Bytes An integer value that corresponds to a size in bytes Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... DecimalDegree A decimal degree expresses latitude or longitude as decimal fractions Double A real number that conforms to the xsd:double specification ExternalIdentifier A CURIE representing an external identifier Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer LanguageCode A language code conforming to ISO_639-1 Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Unit Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"#subsets","title":"Subsets","text":"Subset Description"},{"location":"AnalysisTypeEnum/","title":"Enum: AnalysisTypeEnum","text":"URI: AnalysisTypeEnum
"},{"location":"AnalysisTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metabolomics None metagenomics None Standard short-read metagenomic sequencing metagenomics_long_read None Long-read metagenomic sequencing metaproteomics None metatranscriptomics None natural organic matter None bulk chemistry None amplicon sequencing assay OBI:0002767"},{"location":"AnalysisTypeEnum/#slots","title":"Slots","text":"Name Description analysis_type Select all the data types associated or available for this biosample"},{"location":"AnalysisTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AnalysisTypeEnum/#schema-source","title":"Schema Source","text":"name: AnalysisTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metabolomics:\n text: metabolomics\n metagenomics:\n text: metagenomics\n description: Standard short-read metagenomic sequencing\n title: Metagenomics\n metagenomics_long_read:\n text: metagenomics_long_read\n description: Long-read metagenomic sequencing\n title: Metagenomics (long read)\n metaproteomics:\n text: metaproteomics\n metatranscriptomics:\n text: metatranscriptomics\n natural organic matter:\n text: natural organic matter\n bulk chemistry:\n text: bulk chemistry\n amplicon sequencing assay:\n text: amplicon sequencing assay\n meaning: OBI:0002767\n title: Amplicon sequencing assay\n\nURI: ArchStrucEnum
"},{"location":"ArchStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building None shed None home None"},{"location":"ArchStrucEnum/#slots","title":"Slots","text":"Name Description arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c..."},{"location":"ArchStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ArchStrucEnum/#schema-source","title":"Schema Source","text":"name: arch_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n building:\n text: building\n shed:\n text: shed\n home:\n text: home\n\nThe value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:AttributeValue
classDiagram\n class AttributeValue\n click AttributeValue href \"../AttributeValue\"\n AttributeValue <|-- QuantityValue\n click QuantityValue href \"../QuantityValue\"\n AttributeValue <|-- ImageValue\n click ImageValue href \"../ImageValue\"\n AttributeValue <|-- PersonValue\n click PersonValue href \"../PersonValue\"\n AttributeValue <|-- TextValue\n click TextValue href \"../TextValue\"\n AttributeValue <|-- TimestampValue\n click TimestampValue href \"../TimestampValue\"\n AttributeValue <|-- ControlledTermValue\n click ControlledTermValue href \"../ControlledTermValue\"\n AttributeValue <|-- GeolocationValue\n click GeolocationValue href \"../GeolocationValue\"\n\n\n\n AttributeValue : has_raw_value\n\n AttributeValue : type\n\n\n\nname: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- has_raw_value\n- type\nclass_uri: nmdc:AttributeValue\n\nname: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: AttributeValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: AttributeValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:AttributeValue\n\nURI: BinQualityEnum
"},{"location":"BinQualityEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description HQ None Metagenome-assembled genome is high quality based on MIMAG standards (https:/... MQ None Metagenome-assembled genome is medium quality based on MIMAG standards (https... LQ None Metagenome-assembled genome is low quality based on MIMAG standards (https://..."},{"location":"BinQualityEnum/#slots","title":"Slots","text":"Name Description bin_quality The quality of the metagenome-assembled genome based on MIMAG standards (http..."},{"location":"BinQualityEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BinQualityEnum/#schema-source","title":"Schema Source","text":"name: BinQualityEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n HQ:\n text: HQ\n description: Metagenome-assembled genome is high quality based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893)\n aliases:\n - high quality\n MQ:\n text: MQ\n description: Metagenome-assembled genome is medium quality based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893)\n aliases:\n - medium quality\n LQ:\n text: LQ\n description: Metagenome-assembled genome is low quality based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893)\n aliases:\n - low quality\n\nURI: BiolStatEnum
"},{"location":"BiolStatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description wild None natural None semi-natural None inbred line None breeder's line None hybrid None clonal selection None mutant None"},{"location":"BiolStatEnum/#slots","title":"Slots","text":"Name Description biol_stat The level of genome modification"},{"location":"BiolStatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BiolStatEnum/#schema-source","title":"Schema Source","text":"name: biol_stat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n wild:\n text: wild\n natural:\n text: natural\n semi-natural:\n text: semi-natural\n inbred line:\n text: inbred line\n breeder's line:\n text: breeder's line\n hybrid:\n text: hybrid\n clonal selection:\n text: clonal selection\n mutant:\n text: mutant\n\nBiological source material which can be characterized by an experiment.
URI: nmdc:Biosample
Note
Mermaid class diagram too large to render.
"},{"location":"Biosample/#inheritance","title":"Inheritance","text":"name: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A sample contains information about the sequenced source material.\n Samples are associated with checklists, which define the fields used to annotate\n the samples. Samples are always associated with a taxon.\nnotes:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: Sample\nslots:\n- associated_studies\n- biosample_categories\n- collected_from\n- embargoed\n- host_disease_stat\n- host_taxid\n- img_identifiers\n- neon_biosample_identifiers\n- samp_name\n- gold_biosample_identifiers\n- insdc_biosample_identifiers\n- emsl_biosample_identifiers\n- igsn_biosample_identifiers\n- abs_air_humidity\n- add_recov_method\n- additional_info\n- address\n- adj_room\n- aero_struc\n- agrochem_addition\n- air_PM_concen\n- air_temp\n- air_temp_regm\n- al_sat\n- al_sat_meth\n- alkalinity\n- alkalinity_method\n- alkyl_diethers\n- alt\n- aminopept_act\n- ammonium\n- ammonium_nitrogen\n- amount_light\n- ances_data\n- annual_precpt\n- annual_temp\n- antibiotic_regm\n- api\n- arch_struc\n- aromatics_pc\n- asphaltenes_pc\n- atmospheric_data\n- avg_dew_point\n- avg_occup\n- avg_temp\n- bac_prod\n- bac_resp\n- bacteria_carb_prod\n- barometric_press\n- basin\n- bathroom_count\n- bedroom_count\n- benzene\n- biochem_oxygen_dem\n- biocide\n- biocide_admin_method\n- biol_stat\n- biomass\n- biotic_regm\n- biotic_relationship\n- bishomohopanol\n- blood_press_diast\n- blood_press_syst\n- bromide\n- build_docs\n- build_occup_type\n- building_setting\n- built_struc_age\n- built_struc_set\n- built_struc_type\n- calcium\n- carb_dioxide\n- carb_monoxide\n- carb_nitro_ratio\n- ceil_area\n- ceil_cond\n- ceil_finish_mat\n- ceil_struc\n- ceil_texture\n- ceil_thermal_mass\n- ceil_type\n- ceil_water_mold\n- chem_administration\n- chem_mutagen\n- chem_oxygen_dem\n- chem_treat_method\n- chem_treatment\n- chloride\n- chlorophyll\n- climate_environment\n- collection_date\n- conduc\n- cool_syst_id\n- core field\n- crop_rotation\n- cult_root_med\n- cur_land_use\n- cur_vegetation\n- cur_vegetation_meth\n- date_last_rain\n- density\n- depos_env\n- depth\n- dew_point\n- diether_lipids\n- diss_carb_dioxide\n- diss_hydrogen\n- diss_inorg_carb\n- diss_inorg_nitro\n- diss_inorg_phosp\n- diss_iron\n- diss_org_carb\n- diss_org_nitro\n- diss_oxygen\n- diss_oxygen_fluid\n- dna_cont_well\n- door_comp_type\n- door_cond\n- door_direct\n- door_loc\n- door_mat\n- door_move\n- door_size\n- door_type\n- door_type_metal\n- door_type_wood\n- door_water_mold\n- down_par\n- drainage_class\n- drawings\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- efficiency_percent\n- elev\n- elevator\n- emulsions\n- env_broad_scale\n- env_local_scale\n- env_medium\n- env_package\n- environment field\n- escalator\n- ethylbenzene\n- exp_duct\n- exp_pipe\n- experimental_factor\n- ext_door\n- ext_wall_orient\n- ext_window_orient\n- extreme_event\n- fao_class\n- fertilizer_regm\n- field\n- filter_type\n- fire\n- fireplace_type\n- flooding\n- floor_age\n- floor_area\n- floor_cond\n- floor_count\n- floor_finish_mat\n- floor_struc\n- floor_thermal_mass\n- floor_water_mold\n- fluor\n- freq_clean\n- freq_cook\n- fungicide_regm\n- furniture\n- gaseous_environment\n- gaseous_substances\n- gender_restroom\n- genetic_mod\n- geo_loc_name\n- glucosidase_act\n- gravidity\n- gravity\n- growth_facil\n- growth_habit\n- growth_hormone_regm\n- hall_count\n- handidness\n- hc_produced\n- hcr\n- hcr_fw_salinity\n- hcr_geol_age\n- hcr_pressure\n- hcr_temp\n- heat_cool_type\n- heat_deliv_loc\n- heat_sys_deliv_meth\n- heat_system_id\n- heavy_metals\n- heavy_metals_meth\n- height_carper_fiber\n- herbicide_regm\n- horizon_meth\n- host_age\n- host_body_habitat\n- host_body_product\n- host_body_site\n- host_body_temp\n- host_color\n- host_common_name\n- host_diet\n- host_dry_mass\n- host_family_relation\n- host_genotype\n- host_growth_cond\n- host_height\n- host_last_meal\n- host_length\n- host_life_stage\n- host_phenotype\n- host_sex\n- host_shape\n- host_subject_id\n- host_subspecf_genlin\n- host_substrate\n- host_symbiont\n- host_taxid\n- host_tot_mass\n- host_wet_mass\n- humidity\n- humidity_regm\n- indoor_space\n- indoor_surf\n- indust_eff_percent\n- inorg_particles\n- inside_lux\n- int_wall_cond\n- investigation field\n- iw_bt_date_well\n- iwf\n- last_clean\n- lat_lon\n- lbc_thirty\n- lbceq\n- light_intensity\n- light_regm\n- light_type\n- link_addit_analys\n- link_class_info\n- link_climate_info\n- lithology\n- local_class\n- local_class_meth\n- magnesium\n- manganese\n- max_occup\n- mean_frict_vel\n- mean_peak_frict_vel\n- mech_struc\n- mechanical_damage\n- methane\n- micro_biomass_meth\n- microbial_biomass\n- mineral_nutr_regm\n- misc_param\n- n_alkanes\n- nitrate\n- nitrate_nitrogen\n- nitrite\n- nitrite_nitrogen\n- nitro\n- non_min_nutr_regm\n- nucleic acid sequence source field\n- number_pets\n- number_plants\n- number_resident\n- occup_density_samp\n- occup_document\n- occup_samp\n- org_carb\n- org_count_qpcr_info\n- org_matter\n- org_nitro\n- org_particles\n- organism_count\n- owc_tvdss\n- oxy_stat_samp\n- oxygen\n- part_org_carb\n- part_org_nitro\n- particle_class\n- permeability\n- perturbation\n- pesticide_regm\n- petroleum_hydrocarb\n- ph\n- ph_meth\n- ph_regm\n- phaeopigments\n- phosphate\n- phosplipid_fatt_acid\n- photon_flux\n- plant_growth_med\n- plant_product\n- plant_sex\n- plant_struc\n- pollutants\n- porosity\n- potassium\n- pour_point\n- pre_treatment\n- pres_animal_insect\n- pressure\n- prev_land_use_meth\n- previous_land_use\n- primary_prod\n- primary_treatment\n- prod_rate\n- prod_start_date\n- profile_position\n- quad_pos\n- radiation_regm\n- rainfall_regm\n- reactor_type\n- redox_potential\n- rel_air_humidity\n- rel_humidity_out\n- rel_samp_loc\n- reservoir\n- resins_pc\n- room_air_exch_rate\n- room_architec_elem\n- room_condt\n- room_connected\n- room_count\n- room_dim\n- room_door_dist\n- room_door_share\n- room_hallway\n- room_loc\n- room_moist_dam_hist\n- room_net_area\n- room_occup\n- room_samp_pos\n- room_type\n- room_vol\n- room_wall_share\n- room_window_count\n- root_cond\n- root_med_carbon\n- root_med_macronutr\n- root_med_micronutr\n- root_med_ph\n- root_med_regl\n- root_med_solid\n- root_med_suppl\n- salinity\n- salinity_meth\n- salt_regm\n- samp_capt_status\n- samp_collec_device\n- samp_collec_method\n- samp_collect_point\n- samp_dis_stage\n- samp_floor\n- samp_loc_corr_rate\n- samp_mat_process\n- samp_md\n- samp_name\n- samp_preserv\n- samp_room_id\n- samp_size\n- samp_sort_meth\n- samp_store_dur\n- samp_store_loc\n- samp_store_temp\n- samp_subtype\n- samp_taxon_id\n- samp_time_out\n- samp_transport_cond\n- samp_tvdss\n- samp_type\n- samp_weather\n- samp_well_name\n- saturates_pc\n- season\n- season_environment\n- season_precpt\n- season_temp\n- season_use\n- secondary_treatment\n- sediment_type\n- sequencing field\n- sewage_type\n- shad_dev_water_mold\n- shading_device_cond\n- shading_device_loc\n- shading_device_mat\n- shading_device_type\n- sieving\n- silicate\n- size_frac\n- size_frac_low\n- size_frac_up\n- slope_aspect\n- slope_gradient\n- sludge_retent_time\n- sodium\n- soil_horizon\n- soil_text_measure\n- soil_texture_meth\n- soil_type\n- soil_type_meth\n- solar_irradiance\n- soluble_inorg_mat\n- soluble_org_mat\n- soluble_react_phosp\n- source_mat_id\n- space_typ_state\n- specific\n- specific_ecosystem\n- specific_humidity\n- sr_dep_env\n- sr_geol_age\n- sr_kerog_type\n- sr_lithology\n- standing_water_regm\n- store_cond\n- substructure_type\n- sulfate\n- sulfate_fw\n- sulfide\n- surf_air_cont\n- surf_humidity\n- surf_material\n- surf_moisture\n- surf_moisture_ph\n- surf_temp\n- suspend_part_matter\n- suspend_solids\n- tan\n- temp\n- temp_out\n- tertiary_treatment\n- tidal_stage\n- tillage\n- tiss_cult_growth_med\n- toluene\n- tot_carb\n- tot_depth_water_col\n- tot_diss_nitro\n- tot_inorg_nitro\n- tot_iron\n- tot_nitro\n- tot_nitro_cont_meth\n- tot_nitro_content\n- tot_org_c_meth\n- tot_org_carb\n- tot_part_carb\n- tot_phosp\n- tot_phosphate\n- tot_sulfur\n- train_line\n- train_stat_loc\n- train_stop_loc\n- turbidity\n- tvdss_of_hcr_press\n- tvdss_of_hcr_temp\n- typ_occup_density\n- ventilation_rate\n- ventilation_type\n- vfa\n- vfa_fw\n- vis_media\n- viscosity\n- volatile_org_comp\n- wall_area\n- wall_const_type\n- wall_finish_mat\n- wall_height\n- wall_loc\n- wall_surf_treatment\n- wall_texture\n- wall_thermal_mass\n- wall_water_mold\n- wastewater_type\n- water_cont_soil_meth\n- water_content\n- water_current\n- water_cut\n- water_feat_size\n- water_feat_type\n- water_prod_rate\n- water_temp_regm\n- watering_regm\n- weekday\n- win\n- wind_direction\n- wind_speed\n- window_cond\n- window_cover\n- window_horiz_pos\n- window_loc\n- window_mat\n- window_open_freq\n- window_size\n- window_status\n- window_type\n- window_vert_pos\n- window_water_mold\n- xylene\n- zinc\n- ecosystem\n- ecosystem_category\n- ecosystem_type\n- ecosystem_subtype\n- specific_ecosystem\n- add_date\n- community\n- habitat\n- host_name\n- location\n- mod_date\n- ncbi_taxonomy_name\n- proport_woa_temperature\n- salinity_category\n- sample_collection_site\n- soluble_iron_micromol\n- subsurface_depth\n- air_temp_regm\n- biotic_regm\n- biotic_relationship\n- climate_environment\n- experimental_factor\n- gaseous_environment\n- growth_facil\n- humidity_regm\n- light_regm\n- phosphate\n- samp_collec_method\n- samp_size\n- source_mat_id\n- watering_regm\n- dna_absorb1\n- dna_absorb2\n- dna_collect_site\n- dna_concentration\n- dna_cont_type\n- dna_cont_well\n- dna_container_id\n- dna_dnase\n- dna_isolate_meth\n- dna_organisms\n- dna_project_contact\n- dna_samp_id\n- dna_sample_format\n- dna_sample_name\n- dna_seq_project\n- dna_seq_project_pi\n- dna_seq_project_name\n- dna_volume\n- proposal_dna\n- dnase_rna\n- proposal_rna\n- rna_absorb1\n- rna_absorb2\n- rna_collect_site\n- rna_concentration\n- rna_cont_type\n- rna_cont_well\n- rna_container_id\n- rna_isolate_meth\n- rna_organisms\n- rna_project_contact\n- rna_samp_id\n- rna_sample_format\n- rna_sample_name\n- rna_seq_project\n- rna_seq_project_pi\n- rna_seq_project_name\n- rna_volume\n- collection_date_inc\n- collection_time\n- collection_time_inc\n- experimental_factor_other\n- filter_method\n- isotope_exposure\n- micro_biomass_c_meth\n- micro_biomass_n_meth\n- microbial_biomass_c\n- microbial_biomass_n\n- non_microb_biomass\n- non_microb_biomass_method\n- org_nitro_method\n- other_treatment\n- start_date_inc\n- start_time_inc\n- project_id\n- replicate_number\n- sample_shipped\n- sample_type\n- technical_reps\n- analysis_type\n- sample_link\n- bulk_elect_conductivity\n- infiltrations\n- zinc\n- manganese\n- ammonium_nitrogen\n- nitrate_nitrogen\n- nitrite_nitrogen\n- lbc_thirty\n- lbceq\nslot_usage:\n collected_from:\n name: collected_from\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n elev:\n name: elev\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n range: float\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n alternative_identifiers:\n name: alternative_identifiers\n description: A uriorcurie reference to an external database or resource that provides\n additional information or context about a specific entity at NMDC.\n multivalued: true\n lat_lon:\n name: lat_lon\n notes:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n env_broad_scale:\n name: env_broad_scale\n required: true\n env_local_scale:\n name: env_local_scale\n required: true\n env_medium:\n name: env_medium\n required: true\n associated_studies:\n name: associated_studies\n range: Study\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n range: string\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n examples:\n - value: 1980-05-18, volcanic eruption\n range: string\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n slope_gradient:\n name: slope_gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n annual_precpt:\n name: annual_precpt\n examples:\n - value: 8.94 inch\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n todos:\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n cur_vegetation_meth:\n name: cur_vegetation_meth\n todos:\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n heavy_metals_meth:\n name: heavy_metals_meth\n title: heavy metals method/ extreme unusual properties\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n multivalued: true\n season_precpt:\n name: season_precpt\n title: average seasonal precipitation\n todos:\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n water_cont_soil_meth:\n name: water_cont_soil_meth\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n range: string\n multivalued: true\n ph_meth:\n name: ph_meth\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n tot_carb:\n name: tot_carb\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n tot_nitro_content:\n name: tot_nitro_content\n examples:\n - value: 5 mg N/ L\n tot_org_c_meth:\n name: tot_org_c_meth\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n tot_org_carb:\n name: tot_org_carb\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n salinity_meth:\n name: salinity_meth\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n sieving:\n name: sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n climate_environment:\n name: climate_environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n gaseous_environment:\n name: gaseous_environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n watering_regm:\n name: watering_regm\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\nclass_uri: nmdc:Biosample\nunique_keys:\n samp_name_unique_key:\n unique_key_name: samp_name_unique_key\n unique_key_slots:\n - samp_name\nrules:\n- preconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: dna_well_requires_plate\n- preconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n description: DNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: dna_plate_requires_well\n- preconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: rna_well_requires_plate\n- preconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n description: RNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: rna_plate_requires_well\n\nname: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A sample contains information about the sequenced source material.\n Samples are associated with checklists, which define the fields used to annotate\n the samples. Samples are always associated with a taxon.\nnotes:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: Sample\nslot_usage:\n collected_from:\n name: collected_from\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n elev:\n name: elev\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n range: float\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n alternative_identifiers:\n name: alternative_identifiers\n description: A uriorcurie reference to an external database or resource that provides\n additional information or context about a specific entity at NMDC.\n multivalued: true\n lat_lon:\n name: lat_lon\n notes:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n env_broad_scale:\n name: env_broad_scale\n required: true\n env_local_scale:\n name: env_local_scale\n required: true\n env_medium:\n name: env_medium\n required: true\n associated_studies:\n name: associated_studies\n range: Study\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n range: string\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n examples:\n - value: 1980-05-18, volcanic eruption\n range: string\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n slope_gradient:\n name: slope_gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n annual_precpt:\n name: annual_precpt\n examples:\n - value: 8.94 inch\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n todos:\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n cur_vegetation_meth:\n name: cur_vegetation_meth\n todos:\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n heavy_metals_meth:\n name: heavy_metals_meth\n title: heavy metals method/ extreme unusual properties\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n multivalued: true\n season_precpt:\n name: season_precpt\n title: average seasonal precipitation\n todos:\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n water_cont_soil_meth:\n name: water_cont_soil_meth\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n range: string\n multivalued: true\n ph_meth:\n name: ph_meth\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n tot_carb:\n name: tot_carb\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n tot_nitro_content:\n name: tot_nitro_content\n examples:\n - value: 5 mg N/ L\n tot_org_c_meth:\n name: tot_org_c_meth\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n tot_org_carb:\n name: tot_org_carb\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n salinity_meth:\n name: salinity_meth\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n sieving:\n name: sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n climate_environment:\n name: climate_environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n gaseous_environment:\n name: gaseous_environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n watering_regm:\n name: watering_regm\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\nattributes:\n associated_studies:\n name: associated_studies\n description: The study associated with a resource.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: associated_studies\n owner: Biosample\n domain_of:\n - Biosample\n - DataGeneration\n range: Study\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n biosample_categories:\n name: biosample_categories\n title: Categories the biosample belongs to\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: biosample_categories\n owner: Biosample\n domain_of:\n - Biosample\n range: BiosampleCategoryEnum\n multivalued: true\n collected_from:\n name: collected_from\n description: The Site from which a Biosample was collected\n todos:\n - add an OBO slot_uri ?\n comments:\n - this illustrates implementing a Biosample relation with a (binary) slot\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: collected_from\n owner: Biosample\n domain_of:\n - Biosample\n range: FieldResearchSite\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n embargoed:\n name: embargoed\n description: If true, the data are embargoed and not available for public access.\n todos:\n - make this required?\n - first apply to Biosample\n - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n - applying to a Study may not be granular enough\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: embargoed\n owner: Biosample\n domain_of:\n - Biosample\n range: boolean\n recommended: true\n host_disease_stat:\n name: host_disease_stat\n annotations:\n expected_value:\n tag: expected_value\n value: disease name or Disease Ontology term\n description: List of diseases with which the host has been diagnosed; can include\n multiple diagnoses. The value of the field depends on host; for humans the terms\n should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,\n non-human host diseases are free text\n title: host disease status\n examples:\n - value: rabies [DOID:11260]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host disease status\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000031\n alias: host_disease_stat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_taxid:\n name: host_taxid\n annotations:\n expected_value:\n tag: expected_value\n value: NCBI taxon identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: NCBI taxon id of the host, e.g. 9606\n title: host taxid\n comments:\n - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host taxid\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000250\n alias: host_taxid\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n multivalued: false\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: Biosample\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n neon_biosample_identifiers:\n name: neon_biosample_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - neon_identifiers\n alias: neon_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n samp_name:\n name: samp_name\n annotations:\n expected_value:\n tag: expected_value\n value: text\n description: A local identifier or name that for the material sample used for\n extracting nucleic acids, and subsequent sequencing. It can refer either to\n the original material collected or to any derived sub-samples. It can have any\n format, but we suggest that you make it concise, unique and consistent within\n your lab, and as informative as possible. INSDC requires every sample name from\n a single Submitter to be unique. Use of a globally unique identifier for the\n field source_mat_id is recommended in addition to sample_name.\n title: sample name\n examples:\n - value: ISDsoil1\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample name\n rank: 1000\n is_a: investigation field\n string_serialization: '{text}'\n slot_uri: MIXS:0001107\n alias: samp_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n examples:\n - value: https://bioregistry.io/gold:Gb0312930\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - gold_identifiers\n alias: gold_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: uriorcurie\n multivalued: true\n pattern: ^gold:Gb[0-9]+$\n insdc_biosample_identifiers:\n name: insdc_biosample_identifiers\n description: identifiers for corresponding sample in INSDC\n examples:\n - value: https://bioregistry.io/biosample:SAMEA5989477\n - value: https://bioregistry.io/biosample:SAMD00212331\n description: I13_N_5-10 sample from Soil fungal diversity along elevational\n gradients\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/bioregistry/bioregistry/issues/108\n - https://www.ebi.ac.uk/biosamples/\n - https://www.ncbi.nlm.nih.gov/biosample\n - https://www.ddbj.nig.ac.jp/biosample/index-e.html\n aliases:\n - EBI biosample identifiers\n - NCBI biosample identifiers\n - DDBJ biosample identifiers\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n multivalued: true\n pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n emsl_biosample_identifiers:\n name: emsl_biosample_identifiers\n description: A list of identifiers for the biosample from the EMSL database. This\n is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n EMSL NEXUS database.\n title: EMSL Biosample Identifiers\n todos:\n - removed \"planned\" once NEXUS is online\n - determine real expansion for emsl prefix\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - emsl_identifiers\n alias: emsl_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n igsn_biosample_identifiers:\n name: igsn_biosample_identifiers\n description: A list of identifiers for the biosample from the IGSN database.\n title: IGSN Biosample Identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - igsn_identifiers\n alias: igsn_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n abs_air_humidity:\n name: abs_air_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram, kilogram per kilogram, kilogram, pound\n occurrence:\n tag: occurrence\n value: '1'\n description: Actual mass of water vapor - mh20 - present in the air water vapor\n mixture\n title: absolute air humidity\n examples:\n - value: 9 gram per gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - absolute air humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000122\n alias: abs_air_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n add_recov_method:\n name: add_recov_method\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n for increase of hydrocarbon recovery from resource and start date for each one\n of them. If \"other\" is specified, please propose entry in \"additional info\"\n field\n title: secondary and tertiary recovery methods and start date\n examples:\n - value: Polymer Addition;2018-06-21T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - secondary and tertiary recovery methods and start date\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001009\n alias: add_recov_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n additional_info:\n name: additional_info\n annotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information that doesn't fit anywhere else. Can also be used to propose\n new entries for fields with controlled vocabulary\n title: additional info\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - additional info\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000300\n alias: additional_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n address:\n name: address\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The street name and building number where the sampling occurred.\n title: address\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - address\n rank: 1000\n is_a: core field\n string_serialization: '{integer}{text}'\n slot_uri: MIXS:0000218\n alias: address\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n adj_room:\n name: adj_room\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of rooms (room number, room name) immediately adjacent to the\n sampling room\n title: adjacent rooms\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - adjacent rooms\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000219\n alias: adj_room\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n aero_struc:\n name: aero_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Aerospace structures typically consist of thin plates with stiffeners\n for the external surfaces, bulkheads and frames to support the shape and fasteners\n such as welds, rivets, screws and bolts to hold the components together\n title: aerospace structure\n examples:\n - value: plane\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aerospace structure\n rank: 1000\n is_a: core field\n string_serialization: '[plane|glider]'\n slot_uri: MIXS:0000773\n alias: aero_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n agrochem_addition:\n name: agrochem_addition\n annotations:\n expected_value:\n tag: expected_value\n value: agrochemical name;agrochemical amount;timestamp\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Addition of fertilizers, pesticides, etc. - amount and time of applications\n title: history/agrochemical additions\n examples:\n - value: roundup;5 milligram per liter;2018-06-21\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/agrochemical additions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{timestamp}'\n slot_uri: MIXS:0000639\n alias: agrochem_addition\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n air_PM_concen:\n name: air_PM_concen\n annotations:\n expected_value:\n tag: expected_value\n value: particulate matter name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrograms per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances that remain suspended in the air, and\n comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can\n report multiple PM's by entering numeric values preceded by name of PM\n title: air particulate matter concentration\n examples:\n - value: PM2.5;10 microgram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air particulate matter concentration\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000108\n alias: air_PM_concen\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n air_temp:\n name: air_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature of the air at the time of sampling\n title: air temperature\n examples:\n - value: 20 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000124\n alias: air_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n air_temp_regm:\n name: air_temp_regm\n annotations:\n expected_value:\n tag: expected_value\n value: temperature value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to varying temperatures;\n should include the temperature, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include different temperature regimens\n title: air temperature regimen\n examples:\n - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air temperature regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000551\n alias: air_temp_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n al_sat:\n name: al_sat\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - extreme_unusual_properties/Al saturation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000607\n alias: al_sat\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n al_sat_meth:\n name: al_sat_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or URL\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - extreme_unusual_properties/Al saturation method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000324\n alias: al_sat_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n alkalinity:\n name: alkalinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliequivalent per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Alkalinity, the ability of a solution to neutralize acids to the\n equivalence point of carbonate or bicarbonate\n title: alkalinity\n examples:\n - value: 50 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkalinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000421\n alias: alkalinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n alkalinity_method:\n name: alkalinity_method\n annotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: '1'\n description: Method used for alkalinity measurement\n title: alkalinity method\n examples:\n - value: titration\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkalinity method\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000298\n alias: alkalinity_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n alkyl_diethers:\n name: alkyl_diethers\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of alkyl diethers\n title: alkyl diethers\n examples:\n - value: 0.005 mole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkyl diethers\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000490\n alias: alkyl_diethers\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n alt:\n name: alt\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Altitude is a term used to identify heights of objects such as airplanes,\n space shuttles, rockets, atmospheric balloons and heights of places such as\n atmospheric layers and clouds. It is used to measure the height of an object\n which is above the earth's surface. In this context, the altitude measurement\n is the vertical distance between the earth's surface above sea level and the\n sampled position in the air\n title: altitude\n examples:\n - value: 100 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - altitude\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000094\n alias: alt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n aminopept_act:\n name: aminopept_act\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of aminopeptidase activity\n title: aminopeptidase activity\n examples:\n - value: 0.269 mole per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aminopeptidase activity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000172\n alias: aminopept_act\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ammonium:\n name: ammonium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ammonium in the sample\n title: ammonium\n examples:\n - value: 1.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ammonium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000427\n alias: ammonium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ammonium_nitrogen:\n name: ammonium_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ammonium nitrogen in the sample\n title: ammonium nitrogen\n examples:\n - value: 2.3 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - ammonium_nitrogen\n - NH4-N\n rank: 1000\n alias: ammonium_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n amount_light:\n name: amount_light\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux, lumens per square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The unit of illuminance and luminous emittance, measuring luminous\n flux per unit area\n title: amount of light\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - amount of light\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000140\n alias: amount_light\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ances_data:\n name: ances_data\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about either pedigree or other ancestral information\n description (e.g. parental variety in case of mutant or selection), e.g. A/3*B\n (meaning [(A x B) x B] x B)\n title: ancestral data\n examples:\n - value: A/3*B\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ancestral data\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000247\n alias: ances_data\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n annual_precpt:\n name: annual_precpt\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of all annual precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\n title: mean annual precipitation\n examples:\n - value: 8.94 inch\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean annual precipitation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000644\n alias: annual_precpt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n annual_temp:\n name: annual_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Mean annual temperature\n title: mean annual temperature\n examples:\n - value: 12.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean annual temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000642\n alias: annual_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n antibiotic_regm:\n name: antibiotic_regm\n annotations:\n expected_value:\n tag: expected_value\n value: antibiotic name;antibiotic amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving antibiotic administration;\n should include the name of antibiotic, amount administered, treatment regimen\n including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n antibiotic regimens\n title: antibiotic regimen\n examples:\n - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - antibiotic regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000553\n alias: antibiotic_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n api:\n name: api\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degrees API\n occurrence:\n tag: occurrence\n value: '1'\n description: 'API gravity is a measure of how heavy or light a petroleum liquid\n is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.\n 31.1\u00ac\u221e API)'\n title: API gravity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - API gravity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000157\n alias: api\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n arch_struc:\n name: arch_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: An architectural structure is a human-made, free-standing, immobile\n outdoor construction\n title: architectural structure\n examples:\n - value: shed\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - architectural structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000774\n alias: arch_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: arch_struc_enum\n multivalued: false\n aromatics_pc:\n name: aromatics_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: aromatics wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aromatics wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000133\n alias: aromatics_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n asphaltenes_pc:\n name: asphaltenes_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: asphaltenes wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - asphaltenes wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000135\n alias: asphaltenes_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n atmospheric_data:\n name: atmospheric_data\n annotations:\n expected_value:\n tag: expected_value\n value: atmospheric data name;measurement value\n occurrence:\n tag: occurrence\n value: m\n description: Measurement of atmospheric data; can include multiple data\n title: atmospheric data\n examples:\n - value: wind speed;9 knots\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - atmospheric data\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0001097\n alias: atmospheric_data\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n avg_dew_point:\n name: avg_dew_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of dew point measures taken at the beginning of every\n hour over a 24 hour period on the sampling day\n title: average dew point\n examples:\n - value: 25.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average dew point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000141\n alias: avg_dew_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n avg_occup:\n name: avg_occup\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Daily average occupancy of room. Indicate the number of person(s)\n daily occupying the sampling room.\n title: average daily occupancy\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average daily occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000775\n alias: avg_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n avg_temp:\n name: avg_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of temperatures taken at the beginning of every hour\n over a 24 hour period on the sampling day\n title: average temperature\n examples:\n - value: 12.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000142\n alias: avg_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n bac_prod:\n name: bac_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Bacterial production in the water column measured by isotope uptake\n title: bacterial production\n examples:\n - value: 5 milligram per cubic meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000683\n alias: bac_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n bac_resp:\n name: bac_resp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, micromole oxygen per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of bacterial respiration in the water column\n title: bacterial respiration\n examples:\n - value: 300 micromole oxygen per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial respiration\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000684\n alias: bac_resp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n bacteria_carb_prod:\n name: bacteria_carb_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of bacterial carbon production\n title: bacterial carbon production\n examples:\n - value: 2.53 microgram per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial carbon production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000173\n alias: bacteria_carb_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n barometric_press:\n name: barometric_press\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millibar\n occurrence:\n tag: occurrence\n value: '1'\n description: Force per unit area exerted against a surface by the weight of air\n above that surface\n title: barometric pressure\n examples:\n - value: 5 millibar\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - barometric pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000096\n alias: barometric_press\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n basin:\n name: basin\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the basin (e.g. Campos)\n title: basin name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - basin name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000290\n alias: basin\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n bathroom_count:\n name: bathroom_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of bathrooms in the building\n title: bathroom count\n examples:\n - value: '1'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bathroom count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000776\n alias: bathroom_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n bedroom_count:\n name: bedroom_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of bedrooms in the building\n title: bedroom count\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bedroom count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000777\n alias: bedroom_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n benzene:\n name: benzene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of benzene in the sample\n title: benzene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - benzene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000153\n alias: benzene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n biochem_oxygen_dem:\n name: biochem_oxygen_dem\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Amount of dissolved oxygen needed by aerobic biological organisms\n in a body of water to break down organic material present in a given water sample\n at certain temperature over a specific time period\n title: biochemical oxygen demand\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biochemical oxygen demand\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000653\n alias: biochem_oxygen_dem\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n biocide:\n name: biocide\n annotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: List of biocides (commercial name of product and supplier) and date\n of administration\n title: biocide administration\n examples:\n - value: ALPHA 1427;Baker Hughes;2008-01-23\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biocide administration\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text};{timestamp}'\n slot_uri: MIXS:0001011\n alias: biocide\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n biocide_admin_method:\n name: biocide_admin_method\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Method of biocide administration (dose, frequency, duration, time\n elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3\n days)\n title: biocide administration method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biocide administration method\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\n slot_uri: MIXS:0000456\n alias: biocide_admin_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n biol_stat:\n name: biol_stat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The level of genome modification.\n title: biological status\n examples:\n - value: natural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biological status\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000858\n alias: biol_stat\n owner: Biosample\n domain_of:\n - Biosample\n range: biol_stat_enum\n multivalued: false\n biomass:\n name: biomass\n annotations:\n expected_value:\n tag: expected_value\n value: biomass type;measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram\n occurrence:\n tag: occurrence\n value: m\n description: Amount of biomass; should include the name for the part of biomass\n measured, e.g. Microbial, total. Can include multiple measurements\n title: biomass\n examples:\n - value: total;20 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biomass\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000174\n alias: biomass\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n biotic_regm:\n name: biotic_regm\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about treatment(s) involving use of biotic factors, such\n as bacteria, viruses or fungi.\n title: biotic regimen\n examples:\n - value: sample inoculated with Rhizobium spp. Culture\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biotic regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001038\n alias: biotic_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n biotic_relationship:\n name: biotic_relationship\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n description: Description of relationship(s) between the subject organism and other\n organism(s) it is associated with. E.g., parasite on species X; mutualist with\n species Y. The target organism is the subject of the relationship, and the other\n organism(s) is the object\n title: observed biotic relationship\n examples:\n - value: free living\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - observed biotic relationship\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000028\n alias: biotic_relationship\n owner: Biosample\n domain_of:\n - Biosample\n range: biotic_relationship_enum\n multivalued: false\n bishomohopanol:\n name: bishomohopanol\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, microgram per gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of bishomohopanol\n title: bishomohopanol\n examples:\n - value: 14 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bishomohopanol\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000175\n alias: bishomohopanol\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n blood_press_diast:\n name: blood_press_diast\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\n description: Resting diastolic blood pressure, measured as mm mercury\n title: host blood pressure diastolic\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host blood pressure diastolic\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000258\n alias: blood_press_diast\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n blood_press_syst:\n name: blood_press_syst\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\n description: Resting systolic blood pressure, measured as mm mercury\n title: host blood pressure systolic\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host blood pressure systolic\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000259\n alias: blood_press_syst\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n bromide:\n name: bromide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of bromide\n title: bromide\n examples:\n - value: 0.05 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bromide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000176\n alias: bromide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n build_docs:\n name: build_docs\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building design, construction and operation documents\n title: design, construction, and operation documents\n examples:\n - value: maintenance plans\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - design, construction, and operation documents\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000787\n alias: build_docs\n owner: Biosample\n domain_of:\n - Biosample\n range: build_docs_enum\n multivalued: false\n build_occup_type:\n name: build_occup_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: The primary function for which a building or discrete part of a building\n is intended to be used\n title: building occupancy type\n examples:\n - value: market\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - building occupancy type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000761\n alias: build_occup_type\n owner: Biosample\n domain_of:\n - Biosample\n range: build_occup_type_enum\n multivalued: true\n building_setting:\n name: building_setting\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A location (geography) where a building is set\n title: building setting\n examples:\n - value: rural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - building setting\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000768\n alias: building_setting\n owner: Biosample\n domain_of:\n - Biosample\n range: building_setting_enum\n multivalued: false\n built_struc_age:\n name: built_struc_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year\n occurrence:\n tag: occurrence\n value: '1'\n description: The age of the built structure since construction\n title: built structure age\n examples:\n - value: '15'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000145\n alias: built_struc_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n built_struc_set:\n name: built_struc_set\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The characterization of the location of the built structure as high\n or low human density\n title: built structure setting\n examples:\n - value: rural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure setting\n rank: 1000\n is_a: core field\n string_serialization: '[urban|rural]'\n slot_uri: MIXS:0000778\n alias: built_struc_set\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n built_struc_type:\n name: built_struc_type\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: A physical structure that is a body or assemblage of bodies in space\n to form a system capable of supporting loads\n title: built structure type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000721\n alias: built_struc_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n calcium:\n name: calcium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of calcium in the sample\n title: calcium\n examples:\n - value: 0.2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - calcium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000432\n alias: calcium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n carb_dioxide:\n name: carb_dioxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Carbon dioxide (gas) amount or concentration at the time of sampling\n title: carbon dioxide\n examples:\n - value: 410 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon dioxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000097\n alias: carb_dioxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n carb_monoxide:\n name: carb_monoxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Carbon monoxide (gas) amount or concentration at the time of sampling\n title: carbon monoxide\n examples:\n - value: 0.1 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon monoxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000098\n alias: carb_monoxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n carb_nitro_ratio:\n name: carb_nitro_ratio\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Ratio of amount or concentrations of carbon to nitrogen\n title: carbon/nitrogen ratio\n examples:\n - value: '0.417361111'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon/nitrogen ratio\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000310\n alias: carb_nitro_ratio\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ceil_area:\n name: ceil_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The area of the ceiling space within the room\n title: ceiling area\n examples:\n - value: 25 square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000148\n alias: ceil_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ceil_cond:\n name: ceil_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the ceiling at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: ceiling condition\n examples:\n - value: damaged\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000779\n alias: ceil_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_cond_enum\n multivalued: false\n ceil_finish_mat:\n name: ceil_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material used to finish a ceiling\n title: ceiling finish material\n examples:\n - value: stucco\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000780\n alias: ceil_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_finish_mat_enum\n multivalued: false\n ceil_struc:\n name: ceil_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The construction format of the ceiling\n title: ceiling structure\n examples:\n - value: concrete\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling structure\n rank: 1000\n is_a: core field\n string_serialization: '[wood frame|concrete]'\n slot_uri: MIXS:0000782\n alias: ceil_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n ceil_texture:\n name: ceil_texture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The feel, appearance, or consistency of a ceiling surface\n title: ceiling texture\n examples:\n - value: popcorn\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling texture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000783\n alias: ceil_texture\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_texture_enum\n multivalued: false\n ceil_thermal_mass:\n name: ceil_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the ceiling to provide inertia against temperature\n fluctuations. Generally this means concrete that is exposed. A metal deck that\n supports a concrete slab will act thermally as long as it is exposed to room\n air flow\n title: ceiling thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000143\n alias: ceil_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ceil_type:\n name: ceil_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of ceiling according to the ceiling's appearance or construction\n title: ceiling type\n examples:\n - value: coffered\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000784\n alias: ceil_type\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_type_enum\n multivalued: false\n ceil_water_mold:\n name: ceil_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the ceiling\n title: ceiling signs of water/mold\n examples:\n - value: presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000781\n alias: ceil_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n chem_administration:\n name: chem_administration\n annotations:\n expected_value:\n tag: expected_value\n value: CHEBI;timestamp\n occurrence:\n tag: occurrence\n value: m\n description: List of chemical compounds administered to the host or site where\n sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can\n include multiple compounds. For chemical entities of biological interest ontology\n (chebi) (v 163), http://purl.bioontology.org/ontology/chebi\n title: chemical administration\n examples:\n - value: agar [CHEBI:2509];2018-05-11T20:00Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical administration\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]};{timestamp}'\n slot_uri: MIXS:0000751\n alias: chem_administration\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n chem_mutagen:\n name: chem_mutagen\n annotations:\n expected_value:\n tag: expected_value\n value: mutagen name;mutagen amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving use of mutagens; should include the name of mutagen,\n amount administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple mutagen regimens\n title: chemical mutagen\n examples:\n - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical mutagen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000555\n alias: chem_mutagen\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n chem_oxygen_dem:\n name: chem_oxygen_dem\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: A measure of the capacity of water to consume oxygen during the decomposition\n of organic matter and the oxidation of inorganic chemicals such as ammonia and\n nitrite\n title: chemical oxygen demand\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical oxygen demand\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000656\n alias: chem_oxygen_dem\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n chem_treat_method:\n name: chem_treat_method\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Method of chemical administration(dose, frequency, duration, time\n elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1\n hr; 0 days)\n title: chemical treatment method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical treatment method\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\n slot_uri: MIXS:0000457\n alias: chem_treat_method\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n chem_treatment:\n name: chem_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: List of chemical compounds administered upstream the sampling location\n where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n demulsifiers, and other production chemicals etc.). The commercial name of the\n product and name of the supplier should be provided. The date of administration\n should also be included\n title: chemical treatment\n examples:\n - value: ACCENT 1125;DOW;2010-11-17\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text};{timestamp}'\n slot_uri: MIXS:0001012\n alias: chem_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n chloride:\n name: chloride\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of chloride in the sample\n title: chloride\n examples:\n - value: 5000 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chloride\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000429\n alias: chloride\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n chlorophyll:\n name: chlorophyll\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter, microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of chlorophyll\n title: chlorophyll\n examples:\n - value: 5 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chlorophyll\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000177\n alias: chlorophyll\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n climate_environment:\n name: climate_environment\n annotations:\n expected_value:\n tag: expected_value\n value: climate name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to a particular climate; treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n climates\n title: climate environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n examples:\n - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - climate environment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001040\n alias: climate_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n collection_date:\n name: collection_date\n annotations:\n expected_value:\n tag: expected_value\n value: date and time\n description: 'The time of sampling, either as an instance (single point in time)\n or interval. In case no exact time is available, the date/time can be right\n truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\n title: collection date\n examples:\n - value: 2018-05-11T10:00:00+01:00; 2018-05-11\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - collection date\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000011\n alias: collection_date\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n conduc:\n name: conduc\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliSiemens per centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: Electrical conductivity of water\n title: conductivity\n examples:\n - value: 10 milliSiemens per centimeter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - conductivity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000692\n alias: conduc\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n cool_syst_id:\n name: cool_syst_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: The cooling system identifier\n title: cooling system identifier\n examples:\n - value: '12345'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - cooling system identifier\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000785\n alias: cool_syst_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n core field:\n name: core field\n description: basic fields\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: core_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n crop_rotation:\n name: crop_rotation\n annotations:\n expected_value:\n tag: expected_value\n value: crop rotation status;schedule\n occurrence:\n tag: occurrence\n value: '1'\n description: Whether or not crop is rotated, and if yes, rotation schedule\n title: history/crop rotation\n examples:\n - value: yes;R2/2017-01-01/2018-12-31/P6M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/crop rotation\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000318\n alias: crop_rotation\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n cult_root_med:\n name: cult_root_med\n annotations:\n expected_value:\n tag: expected_value\n value: name, PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Name or reference for the hydroponic or in vitro culture rooting\n medium; can be the name of a commonly used medium or reference to a specific\n medium, e.g. Murashige and Skoog medium. If the medium has not been formally\n published, use the rooting medium descriptors.\n title: culture rooting medium\n examples:\n - value: http://himedialabs.com/TD/PT158.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - culture rooting medium\n rank: 1000\n is_a: core field\n string_serialization: '{text}|{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0001041\n alias: cult_root_med\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n cur_land_use:\n name: cur_land_use\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Present state of sample site\n title: current land use\n examples:\n - value: conifers\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current land use\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001080\n alias: cur_land_use\n owner: Biosample\n domain_of:\n - Biosample\n range: cur_land_use_enum\n multivalued: false\n cur_vegetation:\n name: cur_vegetation\n annotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n title: current vegetation\n todos:\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current vegetation\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000312\n alias: cur_vegetation\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n cur_vegetation_meth:\n name: cur_vegetation_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in vegetation classification\n title: current vegetation method\n todos:\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current vegetation method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000314\n alias: cur_vegetation_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n date_last_rain:\n name: date_last_rain\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: The date of the last time it rained\n title: date last rain\n examples:\n - value: 2018-05-11:T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - date last rain\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000786\n alias: date_last_rain\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n density:\n name: density\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter, gram per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: Density of the sample, which is its mass per unit volume (aka volumetric\n mass density)\n title: density\n examples:\n - value: 1000 kilogram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - density\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000435\n alias: density\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n depos_env:\n name: depos_env\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: depositional environment\n examples:\n - value: Continental - Alluvial\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depositional environment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000992\n alias: depos_env\n owner: Biosample\n domain_of:\n - Biosample\n range: depos_env_enum\n multivalued: false\n depth:\n name: depth\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: The vertical distance below local surface, e.g. for sediment or soil\n samples depth is measured from sediment or soil surface, respectively. Depth\n can be reported as an interval for subsurface samples.\n title: depth\n examples:\n - value: 10 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000018\n alias: depth\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n dew_point:\n name: dew_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The temperature to which a given parcel of humid air must be cooled,\n at constant barometric pressure, for water vapor to condense into water.\n title: dew point\n examples:\n - value: 22 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dew point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000129\n alias: dew_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diether_lipids:\n name: diether_lipids\n annotations:\n expected_value:\n tag: expected_value\n value: diether lipid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of diether lipids; can include multiple types of diether\n lipids\n title: diether lipids\n examples:\n - value: 0.2 nanogram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - diether lipids\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000178\n alias: diether_lipids\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n diss_carb_dioxide:\n name: diss_carb_dioxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved carbon dioxide in the sample or liquid\n portion of the sample\n title: dissolved carbon dioxide\n examples:\n - value: 5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved carbon dioxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000436\n alias: diss_carb_dioxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_hydrogen:\n name: diss_hydrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved hydrogen\n title: dissolved hydrogen\n examples:\n - value: 0.3 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved hydrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000179\n alias: diss_hydrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_inorg_carb:\n name: diss_inorg_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Dissolved inorganic carbon concentration in the sample, typically\n measured after filtering the sample using a 0.45 micrometer filter\n title: dissolved inorganic carbon\n examples:\n - value: 2059 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000434\n alias: diss_inorg_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_inorg_nitro:\n name: diss_inorg_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved inorganic nitrogen\n title: dissolved inorganic nitrogen\n examples:\n - value: 761 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000698\n alias: diss_inorg_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_inorg_phosp:\n name: diss_inorg_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved inorganic phosphorus in the sample\n title: dissolved inorganic phosphorus\n examples:\n - value: 56.5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000106\n alias: diss_inorg_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_iron:\n name: diss_iron\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved iron in the sample\n title: dissolved iron\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved iron\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000139\n alias: diss_iron\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_org_carb:\n name: diss_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved organic carbon in the sample, liquid portion\n of the sample, or aqueous phase of the fluid\n title: dissolved organic carbon\n examples:\n - value: 197 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000433\n alias: diss_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_org_nitro:\n name: diss_org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Dissolved organic nitrogen concentration measured as; total dissolved\n nitrogen - NH4 - NO3 - NO2\n title: dissolved organic nitrogen\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000162\n alias: diss_org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_oxygen:\n name: diss_oxygen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved oxygen\n title: dissolved oxygen\n examples:\n - value: 175 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved oxygen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000119\n alias: diss_oxygen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_oxygen_fluid:\n name: diss_oxygen_fluid\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved oxygen in the oil field produced fluids\n as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\n title: dissolved oxygen in fluids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved oxygen in fluids\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000438\n alias: diss_oxygen_fluid\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n dna_cont_well:\n name: dna_cont_well\n title: DNA plate position\n comments:\n - Required when 'plate' is selected for container type.\n - Leave blank if the sample will be shipped in a tube.\n - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n pass validation.\n - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n examples:\n - value: B2\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{96 well plate pos}'\n alias: dna_cont_well\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n door_comp_type:\n name: door_comp_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The composite type of the door\n title: door type, composite\n examples:\n - value: revolving\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, composite\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000795\n alias: door_comp_type\n owner: Biosample\n domain_of:\n - Biosample\n range: door_comp_type_enum\n multivalued: false\n door_cond:\n name: door_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The phsical condition of the door\n title: door condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000788\n alias: door_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: door_cond_enum\n multivalued: false\n door_direct:\n name: door_direct\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The direction the door opens\n title: door direction of opening\n examples:\n - value: inward\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door direction of opening\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000789\n alias: door_direct\n owner: Biosample\n domain_of:\n - Biosample\n range: door_direct_enum\n multivalued: false\n door_loc:\n name: door_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the door in the room\n title: door location\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000790\n alias: door_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: door_loc_enum\n multivalued: false\n door_mat:\n name: door_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The material the door is composed of\n title: door material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000791\n alias: door_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: door_mat_enum\n multivalued: false\n door_move:\n name: door_move\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of movement of the door\n title: door movement\n examples:\n - value: swinging\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door movement\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000792\n alias: door_move\n owner: Biosample\n domain_of:\n - Biosample\n range: door_move_enum\n multivalued: false\n door_size:\n name: door_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The size of the door\n title: door area or size\n examples:\n - value: 2.5 square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door area or size\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000158\n alias: door_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n door_type:\n name: door_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of door material\n title: door type\n examples:\n - value: wooden\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000794\n alias: door_type\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_enum\n multivalued: false\n door_type_metal:\n name: door_type_metal\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of metal door\n title: door type, metal\n examples:\n - value: hollow\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, metal\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000796\n alias: door_type_metal\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_metal_enum\n multivalued: false\n door_type_wood:\n name: door_type_wood\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of wood door\n title: door type, wood\n examples:\n - value: battened\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, wood\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000797\n alias: door_type_wood\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_wood_enum\n multivalued: false\n door_water_mold:\n name: door_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on a door\n title: door signs of water/mold\n examples:\n - value: presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000793\n alias: door_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n down_par:\n name: down_par\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microEinstein per square meter per second, microEinstein per square\n centimeter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Visible waveband radiance and irradiance measurements in the water\n column\n title: downward PAR\n examples:\n - value: 28.71 microEinstein per square meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - downward PAR\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000703\n alias: down_par\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n drainage_class:\n name: drainage_class\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Drainage classification from a standard system such as the USDA system\n title: drainage classification\n examples:\n - value: well\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - drainage classification\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001085\n alias: drainage_class\n owner: Biosample\n domain_of:\n - Biosample\n range: drainage_class_enum\n multivalued: false\n drawings:\n name: drawings\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The buildings architectural drawings; if design is chosen, indicate\n phase-conceptual, schematic, design development, and construction documents\n title: drawings\n examples:\n - value: sketch\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - drawings\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000798\n alias: drawings\n owner: Biosample\n domain_of:\n - Biosample\n range: drawings_enum\n multivalued: false\n ecosystem:\n name: ecosystem\n description: An ecosystem is a combination of a physical environment (abiotic\n factors) and all the organisms (biotic factors) that interact with this environment.\n Ecosystem is in position 1/5 in a GOLD path.\n comments:\n - The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism\n or environmental sample is collected. The three broad groups under Ecosystem\n are Environmental, Host-associated, and Engineered. They represent samples collected\n from a natural environment or from another organism or from engineered environments\n like bioreactors respectively.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_category:\n name: ecosystem_category\n description: Ecosystem categories represent divisions within the ecosystem based\n on specific characteristics of the environment from where an organism or sample\n is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n comments:\n - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or\n phyla and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_category\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_subtype:\n name: ecosystem_subtype\n description: Ecosystem subtypes represent further subdivision of Ecosystem types\n into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n path.\n comments:\n - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n the Ecosystem subtype category.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_subtype\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_type:\n name: ecosystem_type\n description: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still\n broad but specific to the characteristics of a given environment. Ecosystem\n type is in position 3/5 in a GOLD path.\n comments:\n - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_type\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n efficiency_percent:\n name: efficiency_percent\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Percentage of volatile solids removed from the anaerobic digestor\n title: efficiency percent\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - efficiency percent\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000657\n alias: efficiency_percent\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n elev:\n name: elev\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the\n surface, such as an aircraft in flight or a spacecraft in orbit.\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevation\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000093\n alias: elev\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n multivalued: false\n elevator:\n name: elevator\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of elevators within the built structure\n title: elevator count\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevator count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000799\n alias: elevator\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n emulsions:\n name: emulsions\n annotations:\n expected_value:\n tag: expected_value\n value: emulsion name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Amount or concentration of substances such as paints, adhesives,\n mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion\n types\n title: emulsions\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - emulsions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000660\n alias: emulsions\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n env_broad_scale:\n name: env_broad_scale\n annotations:\n expected_value:\n tag: expected_value\n value: The major environment type(s) where the sample was collected. Recommend\n subclasses of biome [ENVO:00000428]. Multiple terms can be separated by\n one or more pipes.\n tooltip:\n tag: tooltip\n value: The biome or major environmental system where the sample or specimen\n originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]\n in the Environment Ontology (ENVO). For host-associated or plant-associated\n samples, use terms from the UBERON or Plant Ontology to describe the broad\n anatomical or morphological context\n description: 'Report the major environmental system the sample or specimen came\n from. The system(s) identified should have a coarse spatial grain, to provide\n the general environmental context of where the sampling was done (e.g. in the\n desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\n EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\n title: broad-scale environmental context\n examples:\n - value: oceanic epipelagic zone biome [ENVO:01000035]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - broad-scale environmental context\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000012\n alias: env_broad_scale\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n multivalued: false\n env_local_scale:\n name: env_local_scale\n annotations:\n expected_value:\n tag: expected_value\n value: Environmental entities having causal influences upon the entity at\n time of sampling.\n tooltip:\n tag: tooltip\n value: The specific environmental entities or features near the sample or\n specimen that significantly influence its characteristics or composition.\n These entities are typically smaller in scale than the broad environmental\n context. Values for this field should be countable, material nouns and must\n be chosen from subclasses of BFO:0000040 (material entity) that appear in\n the Environment Ontology (ENVO). For host-associated or plant-associated\n samples, use terms from the UBERON or Plant Ontology to describe specific\n anatomical structures or plant parts.\n description: 'Report the entity or entities which are in the sample or specimen\u2019s\n local vicinity and which you believe have significant causal influences on your\n sample or specimen. We recommend using EnvO terms which are of smaller spatial\n grain than your entry for env_broad_scale. Terms, such as anatomical sites,\n from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)\n are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\n title: local environmental context\n examples:\n - value: litter layer [ENVO:01000338]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - local environmental context\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000013\n alias: env_local_scale\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n multivalued: false\n env_medium:\n name: env_medium\n annotations:\n expected_value:\n tag: expected_value\n value: The material displaced by the entity at time of sampling. Recommend\n subclasses of environmental material [ENVO:00010483].\n tooltip:\n tag: tooltip\n value: The predominant environmental material or substrate that directly surrounds\n or hosts the sample or specimen at the time of sampling. Choose values from\n subclasses of the 'environmental material' class [ENVO:00010483] in the\n Environment Ontology (ENVO). Values for this field should be measurable\n or mass material nouns, representing continuous environmental materials.\n For host-associated or plant-associated samples, use terms from the UBERON\n or Plant Ontology to indicate a tissue, organ, or plant structure\n description: 'Report the environmental material(s) immediately surrounding the\n sample or specimen at the time of sampling. We recommend using subclasses of\n ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO\n documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n . Terms from other OBO ontologies are permissible as long as they reference\n mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities\n (e.g. a tree, a leaf, a table top).'\n title: environmental medium\n examples:\n - value: soil [ENVO:00001998]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - environmental medium\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000014\n alias: env_medium\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n multivalued: false\n env_package:\n name: env_package\n description: MIxS extension for reporting of measurements and observations obtained\n from one or more of the environments where the sample was obtained. All environmental\n packages listed here are further defined in separate subtables. By giving the\n name of the environmental package, a selection of fields can be made from the\n subtables and can be reported\n notes:\n - no longer in MIxS as of 6.0?\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - environmental package\n rank: 1000\n alias: env_package\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n environment field:\n name: environment field\n description: field describing environmental aspect of a sample\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: environment_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n escalator:\n name: escalator\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of escalators within the built structure\n title: escalator count\n examples:\n - value: '4'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - escalator count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000800\n alias: escalator\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n ethylbenzene:\n name: ethylbenzene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ethylbenzene in the sample\n title: ethylbenzene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ethylbenzene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000155\n alias: ethylbenzene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n exp_duct:\n name: exp_duct\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The amount of exposed ductwork in the room\n title: exposed ductwork\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exposed ductwork\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000144\n alias: exp_duct\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n exp_pipe:\n name: exp_pipe\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of exposed pipes in the room\n title: exposed pipes\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exposed pipes\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000220\n alias: exp_pipe\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n experimental_factor:\n name: experimental_factor\n annotations:\n expected_value:\n tag: expected_value\n value: text or EFO and/or OBI\n description: Experimental factors are essentially the variable aspects of an experiment\n design which can be used to describe an experiment, or set of experiments, in\n an increasingly detailed manner. This field accepts ontology terms from Experimental\n Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For\n a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\n title: experimental factor\n examples:\n - value: time series design [EFO:EFO_0001779]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - experimental factor\n rank: 1000\n is_a: investigation field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000008\n alias: experimental_factor\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n ext_door:\n name: ext_door\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of exterior doors in the built structure\n title: exterior door count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exterior door count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000170\n alias: ext_door\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n ext_wall_orient:\n name: ext_wall_orient\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The orientation of the exterior wall\n title: orientations of exterior wall\n examples:\n - value: northwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - orientations of exterior wall\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000817\n alias: ext_wall_orient\n owner: Biosample\n domain_of:\n - Biosample\n range: ext_wall_orient_enum\n multivalued: false\n ext_window_orient:\n name: ext_window_orient\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The compass direction the exterior window of the room is facing\n title: orientations of exterior window\n examples:\n - value: southwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - orientations of exterior window\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000818\n alias: ext_window_orient\n owner: Biosample\n domain_of:\n - Biosample\n range: ext_window_orient_enum\n multivalued: false\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n description: Unusual physical events that may have affected microbial populations\n title: history/extreme events\n examples:\n - value: 1980-05-18, volcanic eruption\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/extreme events\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000320\n alias: extreme_event\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n fao_class:\n name: fao_class\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification from the FAO World Reference Database for Soil\n Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\n title: soil_taxonomic/FAO classification\n examples:\n - value: Luvisols\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/FAO classification\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001083\n alias: fao_class\n owner: Biosample\n domain_of:\n - Biosample\n range: fao_class_enum\n multivalued: false\n fertilizer_regm:\n name: fertilizer_regm\n annotations:\n expected_value:\n tag: expected_value\n value: fertilizer name;fertilizer amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the use of fertilizers; should\n include the name of fertilizer, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple fertilizer\n regimens\n title: fertilizer regimen\n examples:\n - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fertilizer regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000556\n alias: fertilizer_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n field:\n name: field\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the hydrocarbon field (e.g. Albacora)\n title: field name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - field name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000291\n alias: field\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n filter_type:\n name: filter_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: A device which removes solid particulates or airborne molecular contaminants\n title: filter type\n examples:\n - value: HEPA\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - filter type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000765\n alias: filter_type\n owner: Biosample\n domain_of:\n - Biosample\n range: filter_type_enum\n multivalued: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n description: Historical and/or physical evidence of fire\n title: history/fire\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/fire\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001086\n alias: fire\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n fireplace_type:\n name: fireplace_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A firebox with chimney\n title: fireplace type\n examples:\n - value: wood burning\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fireplace type\n rank: 1000\n is_a: core field\n string_serialization: '[gas burning|wood burning]'\n slot_uri: MIXS:0000802\n alias: fireplace_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n description: Historical and/or physical evidence of flooding\n title: history/flooding\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/flooding\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000319\n alias: flooding\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n floor_age:\n name: floor_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: years, weeks, days\n occurrence:\n tag: occurrence\n value: '1'\n description: The time period since installment of the carpet or flooring\n title: floor age\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000164\n alias: floor_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n floor_area:\n name: floor_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The area of the floor space within the room\n title: floor area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000165\n alias: floor_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n floor_cond:\n name: floor_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the floor at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: floor condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000803\n alias: floor_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_cond_enum\n multivalued: false\n floor_count:\n name: floor_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of floors in the building, including basements and mechanical\n penthouse\n title: floor count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000225\n alias: floor_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n floor_finish_mat:\n name: floor_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The floor covering type; the finished surface that is walked on\n title: floor finish material\n examples:\n - value: carpet\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000804\n alias: floor_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_finish_mat_enum\n multivalued: false\n floor_struc:\n name: floor_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the structural elements and subfloor upon which the finish\n flooring is installed\n title: floor structure\n examples:\n - value: concrete\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000806\n alias: floor_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_struc_enum\n multivalued: false\n floor_thermal_mass:\n name: floor_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the floor to provide inertia against temperature fluctuations\n title: floor thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000166\n alias: floor_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n floor_water_mold:\n name: floor_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew in a room\n title: floor signs of water/mold\n examples:\n - value: ceiling discoloration\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor signs of water/mold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000805\n alias: floor_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_water_mold_enum\n multivalued: false\n fluor:\n name: fluor\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram chlorophyll a per cubic meter, volts\n occurrence:\n tag: occurrence\n value: '1'\n description: Raw or converted fluorescence of water\n title: fluorescence\n examples:\n - value: 2.5 volts\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fluorescence\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000704\n alias: fluor\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n freq_clean:\n name: freq_clean\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration or {text}\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times the sample location is cleaned. Frequency of\n cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\n title: frequency of cleaning\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - frequency of cleaning\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000226\n alias: freq_clean\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n freq_cook:\n name: freq_cook\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times a meal is cooked per week\n title: frequency of cooking\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - frequency of cooking\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000227\n alias: freq_cook\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n fungicide_regm:\n name: fungicide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: fungicide name;fungicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of fungicides; should include\n the name of fungicide, amount administered, treatment regimen including how\n many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple fungicide regimens\n title: fungicide regimen\n examples:\n - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fungicide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000557\n alias: fungicide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n furniture:\n name: furniture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The types of furniture present in the sampled room\n title: furniture\n examples:\n - value: chair\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - furniture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000807\n alias: furniture\n owner: Biosample\n domain_of:\n - Biosample\n range: furniture_enum\n multivalued: false\n gaseous_environment:\n name: gaseous_environment\n annotations:\n expected_value:\n tag: expected_value\n value: gaseous compound name;gaseous compound amount;treatment interval and\n duration\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Use of conditions with differing gaseous environments; should include\n the name of gaseous compound, amount administered, treatment duration, interval\n and total experimental duration; can include multiple gaseous environment regimens\n title: gaseous environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gaseous environment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000558\n alias: gaseous_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n gaseous_substances:\n name: gaseous_substances\n annotations:\n expected_value:\n tag: expected_value\n value: gaseous substance name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Amount or concentration of substances such as hydrogen sulfide, carbon\n dioxide, methane, etc.; can include multiple substances\n title: gaseous substances\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gaseous substances\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000661\n alias: gaseous_substances\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n gender_restroom:\n name: gender_restroom\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The gender type of the restroom\n title: gender of restroom\n examples:\n - value: male\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gender of restroom\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000808\n alias: gender_restroom\n owner: Biosample\n domain_of:\n - Biosample\n range: gender_restroom_enum\n multivalued: false\n genetic_mod:\n name: genetic_mod\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Genetic modifications of the genome of an organism, which may occur\n naturally by spontaneous mutation, or be introduced by some experimental means,\n e.g. specification of a transgene or the gene knocked-out or details of transient\n transfection\n title: genetic modification\n examples:\n - value: aox1A transgenic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - genetic modification\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0000859\n alias: genetic_mod\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n geo_loc_name:\n name: geo_loc_name\n annotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n name'\n description: The geographical origin of the sample as defined by the country or\n sea name followed by specific region name. Country or sea names should be chosen\n from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n (http://purl.bioontology.org/ontology/GAZ)\n title: geographic location (country and/or sea,region)\n examples:\n - value: 'USA: Maryland, Bethesda'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (country and/or sea,region)\n rank: 1000\n is_a: environment field\n string_serialization: '{term}: {term}, {text}'\n slot_uri: MIXS:0000010\n alias: geo_loc_name\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n glucosidase_act:\n name: glucosidase_act\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mol per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of glucosidase activity\n title: glucosidase activity\n examples:\n - value: 5 mol per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - glucosidase activity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000137\n alias: glucosidase_act\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n gravidity:\n name: gravidity\n annotations:\n expected_value:\n tag: expected_value\n value: gravidity status;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Whether or not subject is gravid, and if yes date due or date post-conception,\n specifying which is used\n title: gravidity\n examples:\n - value: yes;due date:2018-05-11\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gravidity\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{timestamp}'\n slot_uri: MIXS:0000875\n alias: gravidity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n gravity:\n name: gravity\n annotations:\n expected_value:\n tag: expected_value\n value: gravity factor value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter per square second, g\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of gravity factor to study\n various types of responses in presence, absence or modified levels of gravity;\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple treatments\n title: gravity\n examples:\n - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gravity\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000559\n alias: gravity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n growth_facil:\n name: growth_facil\n annotations:\n expected_value:\n tag: expected_value\n value: free text or CO\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\n title: growth facility\n examples:\n - value: Growth chamber [CO_715:0000189]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth facility\n rank: 1000\n is_a: core field\n string_serialization: '{text}|{termLabel} {[termID]}'\n slot_uri: MIXS:0001043\n alias: growth_facil\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n growth_habit:\n name: growth_habit\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Characteristic shape, appearance or growth form of a plant species\n title: growth habit\n examples:\n - value: spreading\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth habit\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001044\n alias: growth_habit\n owner: Biosample\n domain_of:\n - Biosample\n range: growth_habit_enum\n multivalued: false\n growth_hormone_regm:\n name: growth_hormone_regm\n annotations:\n expected_value:\n tag: expected_value\n value: growth hormone name;growth hormone amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of growth hormones; should\n include the name of growth hormone, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple growth\n hormone regimens\n title: growth hormone regimen\n examples:\n - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth hormone regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000560\n alias: growth_hormone_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n hall_count:\n name: hall_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The total count of hallways and cooridors in the built structure\n title: hallway/corridor count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hallway/corridor count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000228\n alias: hall_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n handidness:\n name: handidness\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The handidness of the individual sampled\n title: handidness\n examples:\n - value: right handedness\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - handidness\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000809\n alias: handidness\n owner: Biosample\n domain_of:\n - Biosample\n range: handidness_enum\n multivalued: false\n hc_produced:\n name: hc_produced\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n etc). If \"other\" is specified, please propose entry in \"additional info\" field\n title: hydrocarbon type produced\n examples:\n - value: Gas\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon type produced\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000989\n alias: hc_produced\n owner: Biosample\n domain_of:\n - Biosample\n range: hc_produced_enum\n multivalued: false\n hcr:\n name: hcr\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR\n defined as a natural environmental feature containing large amounts of hydrocarbons\n at high concentrations potentially suitable for commercial exploitation. This\n term should not be confused with the Hydrocarbon Occurrence term which also\n includes hydrocarbon-rich environments with currently limited commercial interest\n such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose\n entry in \"additional info\" field\n title: hydrocarbon resource type\n examples:\n - value: Oil Sand\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000988\n alias: hcr\n owner: Biosample\n domain_of:\n - Biosample\n range: hcr_enum\n multivalued: false\n hcr_fw_salinity:\n name: hcr_fw_salinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original formation water salinity (prior to secondary recovery e.g.\n Waterflooding) expressed as TDS\n title: formation water salinity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - formation water salinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000406\n alias: hcr_fw_salinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n hcr_geol_age:\n name: hcr_geol_age\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: hydrocarbon resource geological age\n examples:\n - value: Silurian\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource geological age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000993\n alias: hcr_geol_age\n owner: Biosample\n domain_of:\n - Biosample\n range: hcr_geol_age_enum\n multivalued: false\n hcr_pressure:\n name: hcr_pressure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: atmosphere, kilopascal\n occurrence:\n tag: occurrence\n value: '1'\n description: Original pressure of the hydrocarbon resource\n title: hydrocarbon resource original pressure\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource original pressure\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000395\n alias: hcr_pressure\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n hcr_temp:\n name: hcr_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Original temperature of the hydrocarbon resource\n title: hydrocarbon resource original temperature\n examples:\n - value: 150-295 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource original temperature\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000393\n alias: hcr_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n heat_cool_type:\n name: heat_cool_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Methods of conditioning or heating a room or building\n title: heating and cooling system type\n examples:\n - value: heat pump\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating and cooling system type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000766\n alias: heat_cool_type\n owner: Biosample\n domain_of:\n - Biosample\n range: heat_cool_type_enum\n multivalued: true\n heat_deliv_loc:\n name: heat_deliv_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The location of heat delivery within the room\n title: heating delivery locations\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating delivery locations\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000810\n alias: heat_deliv_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: heat_deliv_loc_enum\n multivalued: false\n heat_sys_deliv_meth:\n name: heat_sys_deliv_meth\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The method by which the heat is delivered through the system\n title: heating system delivery method\n examples:\n - value: radiant\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating system delivery method\n rank: 1000\n is_a: core field\n string_serialization: '[conductive|radiant]'\n slot_uri: MIXS:0000812\n alias: heat_sys_deliv_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n heat_system_id:\n name: heat_system_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: The heating system identifier\n title: heating system identifier\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating system identifier\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000833\n alias: heat_system_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n heavy_metals:\n name: heavy_metals\n annotations:\n expected_value:\n tag: expected_value\n value: heavy metal name;measurement value unit\n preferred_unit:\n tag: preferred_unit\n value: microgram per gram\n occurrence:\n tag: occurrence\n value: m\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - extreme_unusual_properties/heavy metals\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000652\n alias: heavy_metals\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n heavy_metals_meth:\n name: heavy_metals_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining heavy metals\n title: heavy metals method/ extreme unusual properties\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - extreme_unusual_properties/heavy metals method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000343\n alias: heavy_metals_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n height_carper_fiber:\n name: height_carper_fiber\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average carpet fiber height in the indoor environment\n title: height carpet fiber mat\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - height carpet fiber mat\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000167\n alias: height_carper_fiber\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n herbicide_regm:\n name: herbicide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: herbicide name;herbicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of herbicides; information\n about treatment involving use of growth hormones; should include the name of\n herbicide, amount administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include multiple regimens\n title: herbicide regimen\n examples:\n - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - herbicide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000561\n alias: herbicide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n horizon_meth:\n name: horizon_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the horizon\n title: soil horizon method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil horizon method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000321\n alias: horizon_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_age:\n name: host_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year, day, hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Age of host at the time of sampling; relevant scale depends on species\n and study, e.g. Could be seconds for amoebae or centuries for trees\n title: host age\n examples:\n - value: 10 days\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000255\n alias: host_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_body_habitat:\n name: host_body_habitat\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Original body habitat where the sample was obtained from\n title: host body habitat\n examples:\n - value: nasopharynx\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body habitat\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000866\n alias: host_body_habitat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_body_product:\n name: host_body_product\n annotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\n description: Substance produced by the body, e.g. Stool, mucus, where the sample\n was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma\n or https://www.ebi.ac.uk/ols/ontologies/uberon\n title: host body product\n examples:\n - value: mucus [UBERON:0000912]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body product\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000888\n alias: host_body_product\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n host_body_site:\n name: host_body_site\n annotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of body site where the sample was obtained from, such as a specific\n organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\n title: host body site\n examples:\n - value: gill [UBERON:0002535]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body site\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000867\n alias: host_body_site\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n host_body_temp:\n name: host_body_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Core body temperature of the host when sample was collected\n title: host body temperature\n examples:\n - value: 15 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000274\n alias: host_body_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_color:\n name: host_color\n annotations:\n expected_value:\n tag: expected_value\n value: color\n occurrence:\n tag: occurrence\n value: '1'\n description: The color of host\n title: host color\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host color\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000260\n alias: host_color\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_common_name:\n name: host_common_name\n annotations:\n expected_value:\n tag: expected_value\n value: common name\n occurrence:\n tag: occurrence\n value: '1'\n description: Common name of the host.\n title: host common name\n examples:\n - value: human\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host common name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000248\n alias: host_common_name\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_diet:\n name: host_diet\n annotations:\n expected_value:\n tag: expected_value\n value: diet type\n occurrence:\n tag: occurrence\n value: m\n description: Type of diet depending on the host, for animals omnivore, herbivore\n etc., for humans high-fat, meditteranean etc.; can include multiple diet types\n title: host diet\n examples:\n - value: herbivore\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host diet\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000869\n alias: host_diet\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n host_dry_mass:\n name: host_dry_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of dry mass\n title: host dry mass\n examples:\n - value: 500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host dry mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000257\n alias: host_dry_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_family_relation:\n name: host_family_relation\n annotations:\n expected_value:\n tag: expected_value\n value: relationship type;arbitrary identifier\n occurrence:\n tag: occurrence\n value: m\n description: Familial relationships to other hosts in the same study; can include\n multiple relationships\n title: host family relationship\n examples:\n - value: offspring;Mussel25\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host family relationship\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text}'\n slot_uri: MIXS:0000872\n alias: host_family_relation\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n host_genotype:\n name: host_genotype\n annotations:\n expected_value:\n tag: expected_value\n value: genotype\n occurrence:\n tag: occurrence\n value: '1'\n description: Observed genotype\n title: host genotype\n examples:\n - value: C57BL/6\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host genotype\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000365\n alias: host_genotype\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_growth_cond:\n name: host_growth_cond\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Literature reference giving growth conditions of the host\n title: host growth conditions\n examples:\n - value: https://academic.oup.com/icesjms/article/68/2/349/617247\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host growth conditions\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0000871\n alias: host_growth_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_height:\n name: host_height\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The height of subject\n title: host height\n examples:\n - value: 0.1 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host height\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000264\n alias: host_height\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_last_meal:\n name: host_last_meal\n annotations:\n expected_value:\n tag: expected_value\n value: content;duration\n occurrence:\n tag: occurrence\n value: m\n description: Content of last meal and time since feeding; can include multiple\n values\n title: host last meal\n examples:\n - value: corn feed;P2H\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host last meal\n rank: 1000\n is_a: core field\n string_serialization: '{text};{duration}'\n slot_uri: MIXS:0000870\n alias: host_last_meal\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n host_length:\n name: host_length\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The length of subject\n title: host length\n examples:\n - value: 1 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host length\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000256\n alias: host_length\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_life_stage:\n name: host_life_stage\n annotations:\n expected_value:\n tag: expected_value\n value: stage\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of life stage of host\n title: host life stage\n examples:\n - value: adult\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host life stage\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000251\n alias: host_life_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_phenotype:\n name: host_phenotype\n annotations:\n expected_value:\n tag: expected_value\n value: PATO or HP\n occurrence:\n tag: occurrence\n value: '1'\n description: Phenotype of human or other host. For phenotypic quality ontology\n (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.\n For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\n title: host phenotype\n examples:\n - value: elongated [PATO:0001154]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host phenotype\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000874\n alias: host_phenotype\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n host_sex:\n name: host_sex\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Gender or physical sex of the host.\n title: host sex\n examples:\n - value: non-binary\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host sex\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000811\n alias: host_sex\n owner: Biosample\n domain_of:\n - Biosample\n range: host_sex_enum\n multivalued: false\n host_shape:\n name: host_shape\n annotations:\n expected_value:\n tag: expected_value\n value: shape\n occurrence:\n tag: occurrence\n value: '1'\n description: Morphological shape of host\n title: host shape\n examples:\n - value: round\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host shape\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000261\n alias: host_shape\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_subject_id:\n name: host_subject_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: A unique identifier by which each subject can be referred to, de-identified.\n title: host subject id\n examples:\n - value: MPI123\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host subject id\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000861\n alias: host_subject_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_subspecf_genlin:\n name: host_subspecf_genlin\n annotations:\n expected_value:\n tag: expected_value\n value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n e.g. serovar, biotype, ecotype, variety, cultivar.\n occurrence:\n tag: occurrence\n value: m\n description: Information about the genetic distinctness of the host organism below\n the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n or any relevant genetic typing schemes like Group I plasmid. Subspecies should\n not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage\n name and the lineage rank separated by a colon, e.g., biovar:abc123.\n title: host subspecific genetic lineage\n examples:\n - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host subspecific genetic lineage\n rank: 1000\n is_a: core field\n string_serialization: '{rank name}:{text}'\n slot_uri: MIXS:0001318\n alias: host_subspecf_genlin\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n host_substrate:\n name: host_substrate\n annotations:\n expected_value:\n tag: expected_value\n value: substrate name\n occurrence:\n tag: occurrence\n value: '1'\n description: The growth substrate of the host.\n title: host substrate\n examples:\n - value: rock\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host substrate\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000252\n alias: host_substrate\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_symbiont:\n name: host_symbiont\n annotations:\n expected_value:\n tag: expected_value\n value: species name or common name\n occurrence:\n tag: occurrence\n value: m\n description: The taxonomic name of the organism(s) found living in mutualistic,\n commensalistic, or parasitic symbiosis with the specific host.\n title: observed host symbionts\n examples:\n - value: flukeworms\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - observed host symbionts\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001298\n alias: host_symbiont\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n host_tot_mass:\n name: host_tot_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Total mass of the host at collection, the unit depends on host\n title: host total mass\n examples:\n - value: 2500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host total mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000263\n alias: host_tot_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_wet_mass:\n name: host_wet_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of wet mass\n title: host wet mass\n examples:\n - value: 1500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host wet mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000567\n alias: host_wet_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n humidity:\n name: humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Amount of water vapour in the air, at the time of sampling\n title: humidity\n examples:\n - value: 25 gram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000100\n alias: humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n humidity_regm:\n name: humidity_regm\n annotations:\n expected_value:\n tag: expected_value\n value: humidity value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to varying degree\n of humidity; information about treatment involving use of growth hormones; should\n include amount of humidity administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple regimens\n title: humidity regimen\n examples:\n - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - humidity regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000568\n alias: humidity_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n indoor_space:\n name: indoor_space\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A distinguishable space within a structure, the purpose for which\n discrete areas of a building is used\n title: indoor space\n examples:\n - value: foyer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - indoor space\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000763\n alias: indoor_space\n owner: Biosample\n domain_of:\n - Biosample\n range: indoor_space_enum\n multivalued: false\n indoor_surf:\n name: indoor_surf\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Type of indoor surface\n title: indoor surface\n examples:\n - value: wall\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - indoor surface\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000764\n alias: indoor_surf\n owner: Biosample\n domain_of:\n - Biosample\n range: indoor_surf_enum\n multivalued: false\n indust_eff_percent:\n name: indust_eff_percent\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Percentage of industrial effluents received by wastewater treatment\n plant\n title: industrial effluent percent\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - industrial effluent percent\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000662\n alias: indust_eff_percent\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n inorg_particles:\n name: inorg_particles\n annotations:\n expected_value:\n tag: expected_value\n value: inorganic particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of particles such as sand, grit, metal particles, ceramics,\n etc.; can include multiple particles\n title: inorganic particles\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - inorganic particles\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000664\n alias: inorg_particles\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n inside_lux:\n name: inside_lux\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatt per square metre\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded value at sampling time (power density)\n title: inside lux light\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - inside lux light\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000168\n alias: inside_lux\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n int_wall_cond:\n name: int_wall_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the wall at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: interior wall condition\n examples:\n - value: damaged\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - interior wall condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000813\n alias: int_wall_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: int_wall_cond_enum\n multivalued: false\n investigation field:\n name: investigation field\n description: field describing aspect of the investigation/study to which the sample\n belongs\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: investigation_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n iw_bt_date_well:\n name: iw_bt_date_well\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Injection water breakthrough date per well following a secondary\n and/or tertiary recovery\n title: injection water breakthrough date of specific well\n examples:\n - value: '2018-05-11'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - injection water breakthrough date of specific well\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001010\n alias: iw_bt_date_well\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n iwf:\n name: iwf\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: Proportion of the produced fluids derived from injected water at\n the time of sampling. (e.g. 87%)\n title: injection water fraction\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - injection water fraction\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000455\n alias: iwf\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n last_clean:\n name: last_clean\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: The last time the floor was cleaned (swept, mopped, vacuumed)\n title: last time swept/mopped/vacuumed\n examples:\n - value: 2018-05-11:T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - last time swept/mopped/vacuumed\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000814\n alias: last_clean\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n lat_lon:\n name: lat_lon\n annotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\n description: The geographical origin of the sample as defined by latitude and\n longitude. The values should be reported in decimal degrees and in WGS84 system\n title: geographic location (latitude and longitude)\n notes:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n examples:\n - value: 50.586825 6.408977\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (latitude and longitude)\n rank: 1000\n is_a: environment field\n string_serialization: '{float} {float}'\n slot_uri: MIXS:0000009\n alias: lat_lon\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: GeolocationValue\n multivalued: false\n lbc_thirty:\n name: lbc_thirty\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\n description: lime buffer capacity, determined after 30 minute incubation\n title: lime buffer capacity (at 30 minutes)\n comments:\n - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n one pH unit\n examples:\n - value: 543 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\n aliases:\n - lbc_thirty\n - lbc30\n - lime buffer capacity (at 30 minutes)\n rank: 1000\n alias: lbc_thirty\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n lbceq:\n name: lbceq\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\n description: lime buffer capacity, determined at equilibrium after 5 day incubation\n title: lime buffer capacity (after 5 day incubation)\n comments:\n - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n one pH unit\n examples:\n - value: 1575 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - lbceq\n - lime buffer capacity (at 5-day equilibrium)\n rank: 1000\n alias: lbceq\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n light_intensity:\n name: light_intensity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of light intensity\n title: light intensity\n examples:\n - value: 0.3 lux\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light intensity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000706\n alias: light_intensity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n light_regm:\n name: light_regm\n annotations:\n expected_value:\n tag: expected_value\n value: exposure type;light intensity;light quality\n preferred_unit:\n tag: preferred_unit\n value: lux; micrometer, nanometer, angstrom\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about treatment(s) involving exposure to light, including\n both light intensity and quality.\n title: light regimen\n examples:\n - value: incandescant light;10 lux;450 nanometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000569\n alias: light_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n light_type:\n name: light_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Application of light to achieve some practical or aesthetic effect.\n Lighting includes the use of both artificial light sources such as lamps and\n light fixtures, as well as natural illumination by capturing daylight. Can also\n include absence of light\n title: light type\n examples:\n - value: desk lamp\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000769\n alias: light_type\n owner: Biosample\n domain_of:\n - Biosample\n range: light_type_enum\n multivalued: true\n link_addit_analys:\n name: link_addit_analys\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to additional analysis results performed on the sample\n title: links to additional analysis\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - links to additional analysis\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000340\n alias: link_addit_analys\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n link_class_info:\n name: link_class_info\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to digitized soil maps or other soil classification information\n title: link to classification information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - link to classification information\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000329\n alias: link_class_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n link_climate_info:\n name: link_climate_info\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to climate resource\n title: link to climate information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - link to climate information\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000328\n alias: link_climate_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n lithology:\n name: lithology\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: lithology\n examples:\n - value: Volcanic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - lithology\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000990\n alias: lithology\n owner: Biosample\n domain_of:\n - Biosample\n range: lithology_enum\n multivalued: false\n local_class:\n name: local_class\n annotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification based on local soil classification system\n title: soil_taxonomic/local classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000330\n alias: local_class\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n local_class_meth:\n name: local_class_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the local soil classification\n title: soil_taxonomic/local classification method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000331\n alias: local_class_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n magnesium:\n name: magnesium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter, parts per million, micromole per\n kilogram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of magnesium in the sample\n title: magnesium\n examples:\n - value: 52.8 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - magnesium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000431\n alias: magnesium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n manganese:\n name: manganese\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of manganese in the sample\n title: manganese\n examples:\n - value: 24.7 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - manganese\n rank: 1000\n alias: manganese\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n max_occup:\n name: max_occup\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The maximum amount of people allowed in the indoor environment\n title: maximum occupancy\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - maximum occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000229\n alias: max_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n mean_frict_vel:\n name: mean_frict_vel\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of mean friction velocity\n title: mean friction velocity\n examples:\n - value: 0.5 meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean friction velocity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000498\n alias: mean_frict_vel\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n mean_peak_frict_vel:\n name: mean_peak_frict_vel\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of mean peak friction velocity\n title: mean peak friction velocity\n examples:\n - value: 1 meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean peak friction velocity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000502\n alias: mean_peak_frict_vel\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n mech_struc:\n name: mech_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'mechanical structure: a moving structure'\n title: mechanical structure\n examples:\n - value: elevator\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mechanical structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000815\n alias: mech_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: mech_struc_enum\n multivalued: false\n mechanical_damage:\n name: mechanical_damage\n annotations:\n expected_value:\n tag: expected_value\n value: damage type;body site\n occurrence:\n tag: occurrence\n value: m\n description: Information about any mechanical damage exerted on the plant; can\n include multiple damages and sites\n title: mechanical damage\n examples:\n - value: pruning;bark\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mechanical damage\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text}'\n slot_uri: MIXS:0001052\n alias: mechanical_damage\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n methane:\n name: methane\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per billion, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Methane (gas) amount or concentration at the time of sampling\n title: methane\n examples:\n - value: 1800 parts per billion\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - methane\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000101\n alias: methane\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n micro_biomass_meth:\n name: micro_biomass_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining microbial biomass\n title: microbial biomass method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - microbial biomass method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000339\n alias: micro_biomass_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n microbial_biomass:\n name: microbial_biomass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram per kilogram soil\n occurrence:\n tag: occurrence\n value: '1'\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer. If you keep this, you would need\n to have correction factors used for conversion to the final units\n title: microbial biomass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - microbial biomass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000650\n alias: microbial_biomass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n mineral_nutr_regm:\n name: mineral_nutr_regm\n annotations:\n expected_value:\n tag: expected_value\n value: mineral nutrient name;mineral nutrient amount;treatment interval and\n duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the use of mineral supplements;\n should include the name of mineral nutrient, amount administered, treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n mineral nutrient regimens\n title: mineral nutrient regimen\n examples:\n - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mineral nutrient regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000570\n alias: mineral_nutr_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n misc_param:\n name: misc_param\n annotations:\n expected_value:\n tag: expected_value\n value: parameter name;measurement value\n occurrence:\n tag: occurrence\n value: m\n description: Any other measurement performed or parameter collected, that is not\n listed here\n title: miscellaneous parameter\n examples:\n - value: Bicarbonate ion concentration;2075 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - miscellaneous parameter\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000752\n alias: misc_param\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n n_alkanes:\n name: n_alkanes\n annotations:\n expected_value:\n tag: expected_value\n value: n-alkane name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of n-alkanes; can include multiple n-alkanes\n title: n-alkanes\n examples:\n - value: n-hexadecane;100 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - n-alkanes\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000503\n alias: n_alkanes\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n nitrate:\n name: nitrate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrate in the sample\n title: nitrate\n examples:\n - value: 65 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000425\n alias: nitrate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n nitrate_nitrogen:\n name: nitrate_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrate nitrogen in the sample\n title: nitrate_nitrogen\n comments:\n - often below some specified limit of detection\n examples:\n - value: 0.29 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - nitrate_nitrogen\n - NO3-N\n rank: 1000\n alias: nitrate_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitrite:\n name: nitrite\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrite in the sample\n title: nitrite\n examples:\n - value: 0.5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrite\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000426\n alias: nitrite\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n nitrite_nitrogen:\n name: nitrite_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrite nitrogen in the sample\n title: nitrite_nitrogen\n examples:\n - value: 1.2 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - nitrite_nitrogen\n - NO2-N\n rank: 1000\n alias: nitrite_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitro:\n name: nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrogen (total)\n title: nitrogen\n examples:\n - value: 4.2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000504\n alias: nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n non_min_nutr_regm:\n name: non_min_nutr_regm\n annotations:\n expected_value:\n tag: expected_value\n value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the exposure of plant to non-mineral\n nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n nutrient, amount administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include multiple non-mineral nutrient regimens\n title: non-mineral nutrient regimen\n examples:\n - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - non-mineral nutrient regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000571\n alias: non_min_nutr_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n nucleic acid sequence source field:\n name: nucleic acid sequence source field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: nucleic_acid_sequence_source_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n number_pets:\n name: number_pets\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of pets residing in the sampled space\n title: number of pets\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of pets\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000231\n alias: number_pets\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n number_plants:\n name: number_plants\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of plant(s) in the sampling space\n title: number of houseplants\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of houseplants\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000230\n alias: number_plants\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n number_resident:\n name: number_resident\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of individuals currently occupying in the sampling location\n title: number of residents\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of residents\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000232\n alias: number_resident\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n occup_density_samp:\n name: occup_density_samp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Average number of occupants at time of sampling per square footage\n title: occupant density at sampling\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupant density at sampling\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000217\n alias: occup_density_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n occup_document:\n name: occup_document\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of documentation of occupancy\n title: occupancy documentation\n examples:\n - value: estimate\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupancy documentation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000816\n alias: occup_document\n owner: Biosample\n domain_of:\n - Biosample\n range: occup_document_enum\n multivalued: false\n occup_samp:\n name: occup_samp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Number of occupants present at time of sample within the given space\n title: occupancy at sampling\n examples:\n - value: '10'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupancy at sampling\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000772\n alias: occup_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n org_carb:\n name: org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic carbon\n title: organic carbon\n examples:\n - value: 1.5 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000508\n alias: org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n org_count_qpcr_info:\n name: org_count_qpcr_info\n annotations:\n expected_value:\n tag: expected_value\n value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles\n preferred_unit:\n tag: preferred_unit\n value: number of cells per gram (or ml or cm^2)\n occurrence:\n tag: occurrence\n value: '1'\n description: 'If qpcr was used for the cell count, the target gene name, the primer\n sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n 30 cycles)'\n title: organism count qPCR information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organism count qPCR information\n rank: 1000\n is_a: core field\n string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles'\n slot_uri: MIXS:0000099\n alias: org_count_qpcr_info\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n org_matter:\n name: org_matter\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic matter\n title: organic matter\n examples:\n - value: 1.75 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic matter\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000204\n alias: org_matter\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n org_nitro:\n name: org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic nitrogen\n title: organic nitrogen\n examples:\n - value: 4 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000205\n alias: org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n org_particles:\n name: org_particles\n annotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of particles such as faeces, hairs, food, vomit, paper\n fibers, plant material, humus, etc.\n title: organic particles\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic particles\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000665\n alias: org_particles\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n organism_count:\n name: organism_count\n annotations:\n expected_value:\n tag: expected_value\n value: organism name;measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: number of cells per cubic meter, number of cells per milliliter, number\n of cells per cubic centimeter\n occurrence:\n tag: occurrence\n value: m\n description: 'Total cell count of any organism (or group of organisms) per gram,\n volume or area of sample, should include name of organism followed by count.\n The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should\n also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\n title: organism count\n examples:\n - value: total prokaryotes;3.5e7 cells per milliliter;qPCR\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organism count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000103\n alias: organism_count\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n owc_tvdss:\n name: owc_tvdss\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\n title: oil water contact depth\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oil water contact depth\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000405\n alias: owc_tvdss\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n oxy_stat_samp:\n name: oxy_stat_samp\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Oxygenation status of sample\n title: oxygenation status of sample\n examples:\n - value: aerobic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oxygenation status of sample\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000753\n alias: oxy_stat_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: oxy_stat_samp_enum\n multivalued: false\n oxygen:\n name: oxygen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Oxygen (gas) amount or concentration at the time of sampling\n title: oxygen\n examples:\n - value: 600 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oxygen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000104\n alias: oxygen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n part_org_carb:\n name: part_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of particulate organic carbon\n title: particulate organic carbon\n examples:\n - value: 1.92 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particulate organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000515\n alias: part_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n part_org_nitro:\n name: part_org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of particulate organic nitrogen\n title: particulate organic nitrogen\n examples:\n - value: 0.3 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particulate organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000719\n alias: part_org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n particle_class:\n name: particle_class\n annotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: m\n description: Particles are classified, based on their size, into six general categories:clay,\n silt, sand, gravel, cobbles, and boulders; should include amount of particle\n preceded by the name of the particle type; can include multiple values\n title: particle classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particle classification\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000206\n alias: particle_class\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n permeability:\n name: permeability\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: mD\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Measure of the ability of a hydrocarbon resource to allow fluids\n to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\n title: permeability\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - permeability\n rank: 1000\n is_a: core field\n string_serialization: '{integer} - {integer} {unit}'\n slot_uri: MIXS:0000404\n alias: permeability\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n perturbation:\n name: perturbation\n annotations:\n expected_value:\n tag: expected_value\n value: perturbation type name;perturbation interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Type of perturbation, e.g. chemical administration, physical disturbance,\n etc., coupled with perturbation regimen including how many times the perturbation\n was repeated, how long each perturbation lasted, and the start and end time\n of the entire perturbation period; can include multiple perturbation types\n title: perturbation\n examples:\n - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - perturbation\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000754\n alias: perturbation\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n pesticide_regm:\n name: pesticide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: pesticide name;pesticide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of insecticides; should\n include the name of pesticide, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple pesticide\n regimens\n title: pesticide regimen\n examples:\n - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pesticide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000573\n alias: pesticide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n petroleum_hydrocarb:\n name: petroleum_hydrocarb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of petroleum hydrocarbon\n title: petroleum hydrocarbon\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - petroleum hydrocarbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000516\n alias: petroleum_hydrocarb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ph:\n name: ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Ph measurement of the sample, or liquid portion of sample, or aqueous\n phase of the fluid\n title: pH\n examples:\n - value: '7.2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001001\n alias: ph\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n multivalued: false\n ph_meth:\n name: ph_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining ph\n title: pH method\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0001106\n alias: ph_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n ph_regm:\n name: ph_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving exposure of plants to varying\n levels of ph of the growth media, treatment regimen including how many times\n the treatment was repeated, how long each treatment lasted, and the start and\n end time of the entire treatment; can include multiple regimen\n title: pH regimen\n examples:\n - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001056\n alias: ph_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n phaeopigments:\n name: phaeopigments\n annotations:\n expected_value:\n tag: expected_value\n value: phaeopigment name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of phaeopigments; can include multiple phaeopigments\n title: phaeopigments\n examples:\n - value: 2.5 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phaeopigments\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000180\n alias: phaeopigments\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n phosphate:\n name: phosphate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of phosphate\n title: phosphate\n examples:\n - value: 0.7 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phosphate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000505\n alias: phosphate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n phosplipid_fatt_acid:\n name: phosplipid_fatt_acid\n annotations:\n expected_value:\n tag: expected_value\n value: phospholipid fatty acid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per gram, mole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of phospholipid fatty acids; can include multiple values\n title: phospholipid fatty acid\n examples:\n - value: 2.98 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phospholipid fatty acid\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000181\n alias: phosplipid_fatt_acid\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n photon_flux:\n name: photon_flux\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: number of photons per second per unit area\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of photon flux\n title: photon flux\n examples:\n - value: 3.926 micromole photons per second per square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - photon flux\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000725\n alias: photon_flux\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n plant_growth_med:\n name: plant_growth_med\n annotations:\n expected_value:\n tag: expected_value\n value: EO or enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Specification of the media for growing the plants or tissue cultured\n samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in\n vitro liquid culture medium. Recommended value is a specific value from EO:plant\n growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)\n or other controlled vocabulary\n title: plant growth medium\n examples:\n - value: hydroponic plant culture media [EO:0007067]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant growth medium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001057\n alias: plant_growth_med\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n plant_product:\n name: plant_product\n annotations:\n expected_value:\n tag: expected_value\n value: product name\n occurrence:\n tag: occurrence\n value: '1'\n description: Substance produced by the plant, where the sample was obtained from\n title: plant product\n examples:\n - value: xylem sap [PO:0025539]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant product\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001058\n alias: plant_product\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n plant_sex:\n name: plant_sex\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Sex of the reproductive parts on the whole plant, e.g. pistillate,\n staminate, monoecieous, hermaphrodite.\n title: plant sex\n examples:\n - value: Hermaphroditic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant sex\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001059\n alias: plant_sex\n owner: Biosample\n domain_of:\n - Biosample\n range: plant_sex_enum\n multivalued: false\n plant_struc:\n name: plant_struc\n annotations:\n expected_value:\n tag: expected_value\n value: PO\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of plant structure the sample was obtained from; for Plant Ontology\n (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the\n sex of it can be recorded here.\n title: plant structure\n examples:\n - value: epidermis [PO:0005679]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant structure\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0001060\n alias: plant_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n pollutants:\n name: pollutants\n annotations:\n expected_value:\n tag: expected_value\n value: pollutant name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter, microgram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Pollutant types and, amount or concentrations measured at the time\n of sampling; can report multiple pollutants by entering numeric values preceded\n by name of pollutant\n title: pollutants\n examples:\n - value: lead;0.15 microgram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pollutants\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000107\n alias: pollutants\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n porosity:\n name: porosity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value or range\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Porosity of deposited sediment is volume of voids divided by the\n total volume of sample\n title: porosity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - porosity\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000211\n alias: porosity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n potassium:\n name: potassium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of potassium in the sample\n title: potassium\n examples:\n - value: 463 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - potassium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000430\n alias: potassium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n pour_point:\n name: pour_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Temperature at which a liquid becomes semi solid and loses its flow\n characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with\n a high paraffin content, typically found in crude deriving from a larger proportion\n of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\n title: pour point\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pour point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000127\n alias: pour_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n pre_treatment:\n name: pre_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: pre-treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process of pre-treatment removes materials that can be easily\n collected from the raw wastewater\n title: pre-treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pre-treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000348\n alias: pre_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n pres_animal_insect:\n name: pres_animal_insect\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration;count\n occurrence:\n tag: occurrence\n value: '1'\n description: The type and number of animals or insects present in the sampling\n space.\n title: presence of pets, animals, or insects\n examples:\n - value: cat;5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - presence of pets, animals, or insects\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000819\n alias: pres_animal_insect\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n pattern: ^(cat|dog|rodent|snake|other);\\d+$\n pressure:\n name: pressure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: atmosphere\n occurrence:\n tag: occurrence\n value: '1'\n description: Pressure to which the sample is subject to, in atmospheres\n title: pressure\n examples:\n - value: 50 atmosphere\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000412\n alias: pressure\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n prev_land_use_meth:\n name: prev_land_use_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining previous land use and dates\n title: history/previous land use method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/previous land use method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000316\n alias: prev_land_use_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n previous_land_use:\n name: previous_land_use\n annotations:\n expected_value:\n tag: expected_value\n value: land use name;date\n occurrence:\n tag: occurrence\n value: '1'\n description: Previous land use and dates\n title: history/previous land use\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/previous land use\n rank: 1000\n is_a: core field\n string_serialization: '{text};{timestamp}'\n slot_uri: MIXS:0000315\n alias: previous_land_use\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n primary_prod:\n name: primary_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, gram per square meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of primary production, generally measured as isotope\n uptake\n title: primary production\n examples:\n - value: 100 milligram per cubic meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - primary production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000728\n alias: primary_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n primary_treatment:\n name: primary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: primary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process to produce both a generally homogeneous liquid capable\n of being treated biologically and a sludge that can be separately treated or\n processed\n title: primary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - primary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000349\n alias: primary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n prod_rate:\n name: prod_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Oil and/or gas production rates per well (e.g. 524 m3 / day)\n title: production rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - production rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000452\n alias: prod_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n prod_start_date:\n name: prod_start_date\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Date of field's first production\n title: production start date\n examples:\n - value: '2018-05-11'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - production start date\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001008\n alias: prod_start_date\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n profile_position:\n name: profile_position\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Cross-sectional position in the hillslope where sample was collected.sample\n area position in relation to surrounding areas\n title: profile position\n examples:\n - value: summit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - profile position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001084\n alias: profile_position\n owner: Biosample\n domain_of:\n - Biosample\n range: profile_position_enum\n multivalued: false\n quad_pos:\n name: quad_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The quadrant position of the sampling room within the building\n title: quadrant position\n examples:\n - value: West side\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - quadrant position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000820\n alias: quad_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: quad_pos_enum\n multivalued: false\n radiation_regm:\n name: radiation_regm\n annotations:\n expected_value:\n tag: expected_value\n value: radiation type name;radiation amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: rad, gray\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving exposure of plant or a plant\n part to a particular radiation regimen; should include the radiation type, amount\n or intensity administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple radiation regimens\n title: radiation regimen\n examples:\n - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - radiation regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000575\n alias: radiation_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n rainfall_regm:\n name: rainfall_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to a given amount\n of rainfall, treatment regimen including how many times the treatment was repeated,\n how long each treatment lasted, and the start and end time of the entire treatment;\n can include multiple regimens\n title: rainfall regimen\n examples:\n - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rainfall regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000576\n alias: rainfall_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n reactor_type:\n name: reactor_type\n annotations:\n expected_value:\n tag: expected_value\n value: reactor type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Anaerobic digesters can be designed and engineered to operate using\n a number of different process configurations, as batch or continuous, mesophilic,\n high solid or low solid, and single stage or multistage\n title: reactor type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - reactor type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000350\n alias: reactor_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n redox_potential:\n name: redox_potential\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millivolt\n occurrence:\n tag: occurrence\n value: '1'\n description: Redox potential, measured relative to a hydrogen cell, indicating\n oxidation or reduction potential\n title: redox potential\n examples:\n - value: 300 millivolt\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - redox potential\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000182\n alias: redox_potential\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n rel_air_humidity:\n name: rel_air_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Partial vapor and air pressure, density of the vapor and air, or\n by the actual mass of the vapor and air\n title: relative air humidity\n examples:\n - value: 80%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - relative air humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000121\n alias: rel_air_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n rel_humidity_out:\n name: rel_humidity_out\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded outside relative humidity value at the time of sampling\n title: outside relative humidity\n examples:\n - value: 12 per kilogram of air\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - outside relative humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000188\n alias: rel_humidity_out\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n rel_samp_loc:\n name: rel_samp_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The sampling location within the train car\n title: relative sampling location\n examples:\n - value: center of car\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - relative sampling location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000821\n alias: rel_samp_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: rel_samp_loc_enum\n multivalued: false\n reservoir:\n name: reservoir\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the reservoir (e.g. Carapebus)\n title: reservoir name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - reservoir name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000303\n alias: reservoir\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n resins_pc:\n name: resins_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: resins wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - resins wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000134\n alias: resins_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_air_exch_rate:\n name: room_air_exch_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: The rate at which outside air replaces indoor air in a given space\n title: room air exchange rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room air exchange rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000169\n alias: room_air_exch_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n room_architec_elem:\n name: room_architec_elem\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: The unique details and component parts that, together, form the architecture\n of a distinguisahable space within a built structure\n title: room architectural elements\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room architectural elements\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000233\n alias: room_architec_elem\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n room_condt:\n name: room_condt\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The condition of the room at the time of sampling\n title: room condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000822\n alias: room_condt\n owner: Biosample\n domain_of:\n - Biosample\n range: room_condt_enum\n multivalued: false\n room_connected:\n name: room_connected\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: List of rooms connected to the sampling room by a doorway\n title: rooms connected by a doorway\n examples:\n - value: office\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms connected by a doorway\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000826\n alias: room_connected\n owner: Biosample\n domain_of:\n - Biosample\n range: room_connected_enum\n multivalued: false\n room_count:\n name: room_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The total count of rooms in the built structure including all room\n types\n title: room count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000234\n alias: room_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_dim:\n name: room_dim\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The length, width and height of sampling room\n title: room dimensions\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room dimensions\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\n slot_uri: MIXS:0000192\n alias: room_dim\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_door_dist:\n name: room_door_dist\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Distance between doors (meters) in the hallway between the sampling\n room and adjacent rooms\n title: room door distance\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room door distance\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000193\n alias: room_door_dist\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_door_share:\n name: room_door_share\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) sharing a door with the\n sampling room\n title: rooms that share a door with sampling room\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that share a door with sampling room\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000242\n alias: room_door_share\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_hallway:\n name: room_hallway\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) located in the same hallway\n as sampling room\n title: rooms that are on the same hallway\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that are on the same hallway\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000238\n alias: room_hallway\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_loc:\n name: room_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The position of the room within the building\n title: room location in building\n examples:\n - value: interior room\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room location in building\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000823\n alias: room_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: room_loc_enum\n multivalued: false\n room_moist_dam_hist:\n name: room_moist_dam_hist\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The history of moisture damage or mold in the past 12 months. Number\n of events of moisture damage or mold observed\n title: room moisture damage or mold history\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room moisture damage or mold history\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000235\n alias: room_moist_dam_hist\n owner: Biosample\n domain_of:\n - Biosample\n range: integer\n multivalued: false\n room_net_area:\n name: room_net_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square feet, square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The net floor area of sampling room. Net area excludes wall thicknesses\n title: room net area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room net area\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000194\n alias: room_net_area\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_occup:\n name: room_occup\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Count of room occupancy at time of sampling\n title: room occupancy\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000236\n alias: room_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n room_samp_pos:\n name: room_samp_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The horizontal sampling position in the room relative to architectural\n elements\n title: room sampling position\n examples:\n - value: south corner\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room sampling position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000824\n alias: room_samp_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: room_samp_pos_enum\n multivalued: false\n room_type:\n name: room_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The main purpose or activity of the sampling room. A room is any\n distinguishable space within a structure\n title: room type\n examples:\n - value: bathroom\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000825\n alias: room_type\n owner: Biosample\n domain_of:\n - Biosample\n range: room_type_enum\n multivalued: false\n room_vol:\n name: room_vol\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic feet, cubic meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Volume of sampling room\n title: room volume\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room volume\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000195\n alias: room_vol\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_wall_share:\n name: room_wall_share\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) sharing a wall with the\n sampling room\n title: rooms that share a wall with sampling room\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that share a wall with sampling room\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000243\n alias: room_wall_share\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_window_count:\n name: room_window_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Number of windows in the room\n title: room window count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room window count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000237\n alias: room_window_count\n owner: Biosample\n domain_of:\n - Biosample\n range: integer\n multivalued: false\n root_cond:\n name: root_cond\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Relevant rooting conditions such as field plot size, sowing density,\n container dimensions, number of plants per container.\n title: rooting conditions\n examples:\n - value: http://himedialabs.com/TD/PT158.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting conditions\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001061\n alias: root_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_carbon:\n name: root_med_carbon\n annotations:\n expected_value:\n tag: expected_value\n value: carbon source name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Source of organic carbon in the culture rooting medium; e.g. sucrose.\n title: rooting medium carbon\n examples:\n - value: sucrose\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium carbon\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000577\n alias: root_med_carbon\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_macronutr:\n name: root_med_macronutr\n annotations:\n expected_value:\n tag: expected_value\n value: macronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of the culture rooting medium macronutrients (N,P, K,\n Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\n title: rooting medium macronutrients\n examples:\n - value: KH2PO4;170\u00ac\u2020milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium macronutrients\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000578\n alias: root_med_macronutr\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_micronutr:\n name: root_med_micronutr\n annotations:\n expected_value:\n tag: expected_value\n value: micronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of the culture rooting medium micronutrients (Fe, Mn,\n Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\n title: rooting medium micronutrients\n examples:\n - value: H3BO3;6.2\u00ac\u2020milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium micronutrients\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000579\n alias: root_med_micronutr\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_ph:\n name: root_med_ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: pH measurement of the culture rooting medium; e.g. 5.5.\n title: rooting medium pH\n examples:\n - value: '7.5'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001062\n alias: root_med_ph\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n root_med_regl:\n name: root_med_regl\n annotations:\n expected_value:\n tag: expected_value\n value: regulator name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Growth regulators in the culture rooting medium such as cytokinins,\n auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\n title: rooting medium regulators\n examples:\n - value: abscisic acid;0.75 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium regulators\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000581\n alias: root_med_regl\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_solid:\n name: root_med_solid\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Specification of the solidifying agent in the culture rooting medium;\n e.g. agar.\n title: rooting medium solidifier\n examples:\n - value: agar\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium solidifier\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001063\n alias: root_med_solid\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_suppl:\n name: root_med_suppl\n annotations:\n expected_value:\n tag: expected_value\n value: supplement name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Organic supplements of the culture rooting medium, such as vitamins,\n amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n (0.5\u00ac\u2020mg/L).\n title: rooting medium organic supplements\n examples:\n - value: nicotinic acid;0.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium organic supplements\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000580\n alias: root_med_suppl\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n salinity:\n name: salinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: practical salinity unit, percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: The total concentration of all dissolved salts in a liquid or solid\n sample. While salinity can be measured by a complete chemical analysis, this\n method is difficult and time consuming. More often, it is instead derived from\n the conductivity measurement. This is known as practical salinity. These derivations\n compare the specific conductance of the sample to a salinity standard such as\n seawater.\n title: salinity\n examples:\n - value: 25 practical salinity unit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000183\n alias: salinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n salinity_meth:\n name: salinity_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining salinity\n title: salinity method\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salinity method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000341\n alias: salinity_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n salt_regm:\n name: salt_regm\n annotations:\n expected_value:\n tag: expected_value\n value: salt name;salt amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of salts as supplement\n to liquid and soil growth media; should include the name of salt, amount administered,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple salt regimens\n title: salt regimen\n examples:\n - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salt regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000582\n alias: salt_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n samp_capt_status:\n name: samp_capt_status\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Reason for the sample\n title: sample capture status\n examples:\n - value: farm sample\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample capture status\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000860\n alias: samp_capt_status\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_capt_status_enum\n multivalued: false\n samp_collec_device:\n name: samp_collec_device\n annotations:\n expected_value:\n tag: expected_value\n value: device name\n description: The device used to collect an environmental sample. This field accepts\n terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\n title: sample collection device\n examples:\n - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection device\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000002\n alias: samp_collec_device\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n samp_collec_method:\n name: samp_collec_method\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url , or text\n description: The method employed for collecting the sample.\n title: sample collection method\n examples:\n - value: swabbing\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection method\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001225\n alias: samp_collec_method\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n samp_collect_point:\n name: samp_collect_point\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Sampling point on the asset were sample was collected (e.g. Wellhead,\n storage tank, separator, etc). If \"other\" is specified, please propose entry\n in \"additional info\" field\n title: sample collection point\n examples:\n - value: well\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001015\n alias: samp_collect_point\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_collect_point_enum\n multivalued: false\n samp_dis_stage:\n name: samp_dis_stage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Stage of the disease at the time of sample collection, e.g. inoculation,\n penetration, infection, growth and reproduction, dissemination of pathogen.\n title: sample disease stage\n examples:\n - value: infection\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample disease stage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000249\n alias: samp_dis_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_dis_stage_enum\n multivalued: false\n samp_floor:\n name: samp_floor\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The floor of the building, where the sampling room is located\n title: sampling floor\n examples:\n - value: 4th floor\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling floor\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000828\n alias: samp_floor\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_floor_enum\n multivalued: false\n samp_loc_corr_rate:\n name: samp_loc_corr_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: millimeter per year\n occurrence:\n tag: occurrence\n value: '1'\n description: Metal corrosion rate is the speed of metal deterioration due to environmental\n conditions. As environmental conditions change corrosion rates change accordingly.\n Therefore, long term corrosion rates are generally more informative than short\n term rates and for that reason they are preferred during reporting. In the case\n of suspected MIC, corrosion rate measurements at the time of sampling might\n provide insights into the involvement of certain microbial community members\n in MIC as well as potential microbial interplays\n title: corrosion rate at sample location\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - corrosion rate at sample location\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000136\n alias: samp_loc_corr_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_mat_process:\n name: samp_mat_process\n annotations:\n expected_value:\n tag: expected_value\n value: text\n description: A brief description of any processing applied to the sample during\n or after retrieving the sample from environment, or a link to the relevant protocol(s)\n performed.\n title: sample material processing\n examples:\n - value: filtering of seawater, storing samples in ethanol\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample material processing\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{text}'\n slot_uri: MIXS:0000016\n alias: samp_mat_process\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n samp_md:\n name: samp_md\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: In non deviated well, measured depth is equal to the true vertical\n depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated\n wells, the MD is the length of trajectory of the borehole measured from the\n same reference or datum. Common datums used are ground level (GL), drilling\n rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: sample measured depth\n examples:\n - value: 1534 meter;MSL\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample measured depth\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000413\n alias: samp_md\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n samp_preserv:\n name: samp_preserv\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliliter\n occurrence:\n tag: occurrence\n value: '1'\n description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\n title: preservative added to sample\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - preservative added to sample\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000463\n alias: samp_preserv\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_room_id:\n name: samp_room_id\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Sampling room number. This ID should be consistent with the designations\n on the building floor plans\n title: sampling room ID or name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling room ID or name\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000244\n alias: samp_room_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_size:\n name: samp_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, liter\n description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n sample collected.\n title: amount or size of sample collected\n examples:\n - value: 5 liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - amount or size of sample collected\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000001\n alias: samp_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n samp_sort_meth:\n name: samp_sort_meth\n annotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: m\n description: Method by which samples are sorted; open face filter collecting total\n suspended particles, prefilter to remove particles larger than X micrometers\n in diameter, where common values of X would be 10 and 2.5 full size sorting\n in a cascade impactor.\n title: sample size sorting method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample size sorting method\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000216\n alias: samp_sort_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n samp_store_dur:\n name: samp_store_dur\n annotations:\n expected_value:\n tag: expected_value\n value: duration\n occurrence:\n tag: occurrence\n value: '1'\n description: Duration for which the sample was stored\n title: sample storage duration\n examples:\n - value: P1Y6M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage duration\n rank: 1000\n is_a: core field\n string_serialization: '{duration}'\n slot_uri: MIXS:0000116\n alias: samp_store_dur\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_store_loc:\n name: samp_store_loc\n annotations:\n expected_value:\n tag: expected_value\n value: location name\n occurrence:\n tag: occurrence\n value: '1'\n description: Location at which sample was stored, usually name of a specific freezer/room\n title: sample storage location\n examples:\n - value: Freezer no:5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage location\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000755\n alias: samp_store_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_store_temp:\n name: samp_store_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature at which sample was stored, e.g. -80 degree Celsius\n title: sample storage temperature\n examples:\n - value: -80 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000110\n alias: samp_store_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n samp_subtype:\n name: samp_subtype\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of sample sub-type. For example if \"sample type\" is \"Produced\n Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified,\n please propose entry in \"additional info\" field\n title: sample subtype\n examples:\n - value: biofilm\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample subtype\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000999\n alias: samp_subtype\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_subtype_enum\n multivalued: false\n samp_taxon_id:\n name: samp_taxon_id\n annotations:\n expected_value:\n tag: expected_value\n value: Taxonomy ID\n description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa\n sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or\n 'blank sample' for negative controls.\n title: Taxonomy ID of DNA sample\n comments:\n - coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Taxonomy ID of DNA sample\n rank: 1000\n is_a: investigation field\n slot_uri: MIXS:0001320\n alias: samp_taxon_id\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n multivalued: false\n samp_time_out:\n name: samp_time_out\n annotations:\n expected_value:\n tag: expected_value\n value: time\n preferred_unit:\n tag: preferred_unit\n value: hour\n occurrence:\n tag: occurrence\n value: '1'\n description: The recent and long term history of outside sampling\n title: sampling time outside\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling time outside\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000196\n alias: samp_time_out\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_transport_cond:\n name: samp_transport_cond\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: days;degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Sample transport duration (in days or hrs) and temperature the sample\n was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\n title: sample transport conditions\n examples:\n - value: 5 days;-20 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample transport conditions\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000410\n alias: samp_transport_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_tvdss:\n name: samp_tvdss\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value or measurement value range\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Depth of the sample i.e. The vertical distance between the sea level\n and the sampled position in the subsurface. Depth can be reported as an interval\n for subsurface samples e.g. 1325.75-1362.25 m\n title: sample true vertical depth subsea\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample true vertical depth subsea\n rank: 1000\n is_a: core field\n string_serialization: '{float}-{float} {unit}'\n slot_uri: MIXS:0000409\n alias: samp_tvdss\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_type:\n name: samp_type\n annotations:\n expected_value:\n tag: expected_value\n value: GENEPIO:0001246\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material from which the sample was obtained. For the\n Hydrocarbon package, samples include types like core, rock trimmings, drill\n cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,\n produced water, injected water, swabs, etc. For the Food Package, samples are\n usually categorized as food, body products or tissues, or environmental material.\n This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\n title: sample type\n examples:\n - value: built environment sample [GENEPIO:0001248]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000998\n alias: samp_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_weather:\n name: samp_weather\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The weather on the sampling day\n title: sampling day weather\n examples:\n - value: foggy\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling day weather\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000827\n alias: samp_weather\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_weather_enum\n multivalued: false\n samp_well_name:\n name: samp_well_name\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the well (e.g. BXA1123) where sample was taken\n title: sample well name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample well name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000296\n alias: samp_well_name\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n saturates_pc:\n name: saturates_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: saturates wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - saturates wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000131\n alias: saturates_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n season:\n name: season\n annotations:\n expected_value:\n tag: expected_value\n value: NCIT:C94729\n occurrence:\n tag: occurrence\n value: '1'\n description: The season when sampling occurred. Any of the four periods into which\n the year is divided by the equinoxes and solstices. This field accepts terms\n listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).\n title: season\n examples:\n - value: autumn [NCIT:C94733]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - season\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000829\n alias: season\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n season_environment:\n name: season_environment\n annotations:\n expected_value:\n tag: expected_value\n value: seasonal environment name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to a particular season (e.g. Winter,\n summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment\n title: seasonal environment\n examples:\n - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - seasonal environment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001068\n alias: season_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n season_precpt:\n name: season_precpt\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of all seasonal precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\n title: average seasonal precipitation\n todos:\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean seasonal precipitation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000645\n alias: season_precpt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n season_temp:\n name: season_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Mean seasonal temperature\n title: mean seasonal temperature\n examples:\n - value: 18 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean seasonal temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000643\n alias: season_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n season_use:\n name: season_use\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The seasons the space is occupied\n title: seasonal use\n examples:\n - value: Winter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - seasonal use\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000830\n alias: season_use\n owner: Biosample\n domain_of:\n - Biosample\n range: season_use_enum\n multivalued: false\n secondary_treatment:\n name: secondary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: secondary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process for substantially degrading the biological content of\n the sewage\n title: secondary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - secondary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000351\n alias: secondary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n sediment_type:\n name: sediment_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about the sediment type based on major constituents\n title: sediment type\n examples:\n - value: biogenous\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sediment type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001078\n alias: sediment_type\n owner: Biosample\n domain_of:\n - Biosample\n range: sediment_type_enum\n multivalued: false\n sequencing field:\n name: sequencing field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: sequencing_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n sewage_type:\n name: sewage_type\n annotations:\n expected_value:\n tag: expected_value\n value: sewage type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Type of wastewater treatment plant as municipial or industrial\n title: sewage type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sewage type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000215\n alias: sewage_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n shad_dev_water_mold:\n name: shad_dev_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the shading device\n title: shading device signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000834\n alias: shad_dev_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n shading_device_cond:\n name: shading_device_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the shading device at the time of sampling\n title: shading device condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000831\n alias: shading_device_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: shading_device_cond_enum\n multivalued: false\n shading_device_loc:\n name: shading_device_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The location of the shading device in relation to the built structure\n title: shading device location\n examples:\n - value: exterior\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device location\n rank: 1000\n is_a: core field\n string_serialization: '[exterior|interior]'\n slot_uri: MIXS:0000832\n alias: shading_device_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n shading_device_mat:\n name: shading_device_mat\n annotations:\n expected_value:\n tag: expected_value\n value: material name\n occurrence:\n tag: occurrence\n value: '1'\n description: The material the shading device is composed of\n title: shading device material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device material\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000245\n alias: shading_device_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n shading_device_type:\n name: shading_device_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of shading device\n title: shading device type\n examples:\n - value: slatted aluminum awning\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000835\n alias: shading_device_type\n owner: Biosample\n domain_of:\n - Biosample\n range: shading_device_type_enum\n multivalued: false\n sieving:\n name: sieving\n annotations:\n expected_value:\n tag: expected_value\n value: design name and/or size;amount\n occurrence:\n tag: occurrence\n value: '1'\n description: Collection design of pooled samples and/or sieve size and amount\n of sample sieved\n title: composite design/sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - composite design/sieving\n rank: 1000\n is_a: core field\n string_serialization: '{{text}|{float} {unit}};{float} {unit}'\n slot_uri: MIXS:0000322\n alias: sieving\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n silicate:\n name: silicate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of silicate\n title: silicate\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - silicate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000184\n alias: silicate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n size_frac:\n name: size_frac\n annotations:\n expected_value:\n tag: expected_value\n value: filter size value range\n description: Filtering pore size used in sample preparation\n title: size fraction selected\n examples:\n - value: 0-0.22 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size fraction selected\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{float}-{float} {unit}'\n slot_uri: MIXS:0000017\n alias: size_frac\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n size_frac_low:\n name: size_frac_low\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n Materials larger than the size threshold are excluded from the sample\n title: size-fraction lower threshold\n examples:\n - value: 0.2 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size-fraction lower threshold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000735\n alias: size_frac_low\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n size_frac_up:\n name: size_frac_up\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the mesh/pore size used to retain the sample. Materials\n smaller than the size threshold are excluded from the sample\n title: size-fraction upper threshold\n examples:\n - value: 20 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size-fraction upper threshold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000736\n alias: size_frac_up\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n slope_aspect:\n name: slope_aspect\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree\n occurrence:\n tag: occurrence\n value: '1'\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n title: slope aspect\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - slope aspect\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000647\n alias: slope_aspect\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n slope_gradient:\n name: slope_gradient\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Commonly called 'slope'. The angle between ground surface and a horizontal\n line (in percent). This is the direction that overland water would flow. This\n measure is usually taken with a hand level meter or clinometer\n title: slope gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - slope gradient\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000646\n alias: slope_gradient\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sludge_retent_time:\n name: sludge_retent_time\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: hours\n occurrence:\n tag: occurrence\n value: '1'\n description: The time activated sludge remains in reactor\n title: sludge retention time\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sludge retention time\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000669\n alias: sludge_retent_time\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sodium:\n name: sodium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Sodium concentration in the sample\n title: sodium\n examples:\n - value: 10.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sodium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000428\n alias: sodium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n soil_horizon:\n name: soil_horizon\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Specific layer in the land area which measures parallel to the soil\n surface and possesses physical characteristics which differ from the layers\n above and beneath\n title: soil horizon\n examples:\n - value: A horizon\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil horizon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001082\n alias: soil_horizon\n owner: Biosample\n domain_of:\n - Biosample\n range: soil_horizon_enum\n multivalued: false\n soil_text_measure:\n name: soil_text_measure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative proportion of different grain sizes of mineral particles\n in a soil, as described using a standard system; express as % sand (50 um to\n 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty\n clay loam) optional.\n title: soil texture measurement\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil texture measurement\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000335\n alias: soil_text_measure\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n soil_texture_meth:\n name: soil_texture_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining soil texture\n title: soil texture method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil texture method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000336\n alias: soil_texture_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n soil_type:\n name: soil_type\n annotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of the soil type or classification. This field accepts\n terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms\n can be separated by pipes.\n title: soil type\n examples:\n - value: plinthosol [ENVO:00002250]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000332\n alias: soil_type\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n soil_type_meth:\n name: soil_type_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining soil series name or other\n lower-level classification\n title: soil type method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000334\n alias: soil_type_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n solar_irradiance:\n name: solar_irradiance\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatts per square meter per day, ergs per square centimeter per\n second\n occurrence:\n tag: occurrence\n value: '1'\n description: The amount of solar energy that arrives at a specific area of a surface\n during a specific time interval\n title: solar irradiance\n examples:\n - value: 1.36 kilowatts per square meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - solar irradiance\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000112\n alias: solar_irradiance\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n soluble_inorg_mat:\n name: soluble_inorg_mat\n annotations:\n expected_value:\n tag: expected_value\n value: soluble inorganic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances such as ammonia, road-salt, sea-salt,\n cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.\n title: soluble inorganic material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble inorganic material\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000672\n alias: soluble_inorg_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n soluble_org_mat:\n name: soluble_org_mat\n annotations:\n expected_value:\n tag: expected_value\n value: soluble organic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances such as urea, fruit sugars, soluble proteins,\n drugs, pharmaceuticals, etc.\n title: soluble organic material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble organic material\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000673\n alias: soluble_org_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n soluble_react_phosp:\n name: soluble_react_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of soluble reactive phosphorus\n title: soluble reactive phosphorus\n examples:\n - value: 0.1 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble reactive phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000738\n alias: soluble_react_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n source_mat_id:\n name: source_mat_id\n annotations:\n expected_value:\n tag: expected_value\n value: 'for cultures of microorganisms: identifiers for two culture collections;\n for other material a unique arbitrary identifer'\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source material identifiers\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{text}'\n slot_uri: MIXS:0000026\n alias: source_mat_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n space_typ_state:\n name: space_typ_state\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Customary or normal state of the space\n title: space typical state\n examples:\n - value: typically occupied\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - space typical state\n rank: 1000\n is_a: core field\n string_serialization: '[typically occupied|typically unoccupied]'\n slot_uri: MIXS:0000770\n alias: space_typ_state\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n specific:\n name: specific\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'The building specifications. If design is chosen, indicate phase:\n conceptual, schematic, design development, construction documents'\n title: specifications\n examples:\n - value: construction\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - specifications\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000836\n alias: specific\n owner: Biosample\n domain_of:\n - Biosample\n range: specific_enum\n multivalued: false\n specific_ecosystem:\n name: specific_ecosystem\n description: Specific ecosystems represent specific features of the environment\n like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n Specific ecosystem is in position 5/5 in a GOLD path.\n comments:\n - Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: specific_ecosystem\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n specific_humidity:\n name: specific_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\n description: The mass of water vapour in a unit mass of moist air, usually expressed\n as grams of vapour per kilogram of air, or, in air conditioning, as grains per\n pound.\n title: specific humidity\n examples:\n - value: 15 per kilogram of air\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - specific humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000214\n alias: specific_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sr_dep_env:\n name: sr_dep_env\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: source rock depositional environment\n examples:\n - value: Marine\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock depositional environment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000996\n alias: sr_dep_env\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_dep_env_enum\n multivalued: false\n sr_geol_age:\n name: sr_geol_age\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: source rock geological age\n examples:\n - value: Silurian\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock geological age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000997\n alias: sr_geol_age\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_geol_age_enum\n multivalued: false\n sr_kerog_type:\n name: sr_kerog_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic\n and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/\n fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris\n (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: source rock kerogen type\n examples:\n - value: Type IV\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock kerogen type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000994\n alias: sr_kerog_type\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_kerog_type_enum\n multivalued: false\n sr_lithology:\n name: sr_lithology\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: source rock lithology\n examples:\n - value: Coal\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock lithology\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000995\n alias: sr_lithology\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_lithology_enum\n multivalued: false\n standing_water_regm:\n name: standing_water_regm\n annotations:\n expected_value:\n tag: expected_value\n value: standing water type;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to standing water during a plant's\n life span, types can be flood water or standing water, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple regimens\n title: standing water regimen\n examples:\n - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - standing water regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001069\n alias: standing_water_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n store_cond:\n name: store_cond\n annotations:\n expected_value:\n tag: expected_value\n value: storage condition type;duration\n occurrence:\n tag: occurrence\n value: '1'\n description: Explain how and for how long the soil sample was stored before DNA\n extraction (fresh/frozen/other).\n title: storage conditions\n examples:\n - value: -20 degree Celsius freezer;P2Y10D\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - storage conditions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{duration}'\n slot_uri: MIXS:0000327\n alias: store_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n substructure_type:\n name: substructure_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: The substructure or under building is that largely hidden section\n of the building which is built off the foundations to the ground floor level\n title: substructure type\n examples:\n - value: basement\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - substructure type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000767\n alias: substructure_type\n owner: Biosample\n domain_of:\n - Biosample\n range: substructure_type_enum\n multivalued: true\n sulfate:\n name: sulfate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of sulfate in the sample\n title: sulfate\n examples:\n - value: 5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000423\n alias: sulfate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sulfate_fw:\n name: sulfate_fw\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original sulfate concentration in the hydrocarbon resource\n title: sulfate in formation water\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfate in formation water\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000407\n alias: sulfate_fw\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sulfide:\n name: sulfide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of sulfide in the sample\n title: sulfide\n examples:\n - value: 2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000424\n alias: sulfide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n surf_air_cont:\n name: surf_air_cont\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Contaminant identified on surface\n title: surface-air contaminant\n examples:\n - value: radon\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface-air contaminant\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000759\n alias: surf_air_cont\n owner: Biosample\n domain_of:\n - Biosample\n range: surf_air_cont_enum\n multivalued: true\n surf_humidity:\n name: surf_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Surfaces: water activity as a function of air and material moisture'\n title: surface humidity\n examples:\n - value: 10%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000123\n alias: surf_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n surf_material:\n name: surf_material\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Surface materials at the point of sampling\n title: surface material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000758\n alias: surf_material\n owner: Biosample\n domain_of:\n - Biosample\n range: surf_material_enum\n multivalued: false\n surf_moisture:\n name: surf_moisture\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million, gram per cubic meter, gram per square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Water held on a surface\n title: surface moisture\n examples:\n - value: 0.01 gram per square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface moisture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000128\n alias: surf_moisture\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n surf_moisture_ph:\n name: surf_moisture_ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: ph measurement of surface\n title: surface moisture pH\n examples:\n - value: '7'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface moisture pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000760\n alias: surf_moisture_ph\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n multivalued: false\n surf_temp:\n name: surf_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature of the surface at the time of sampling\n title: surface temperature\n examples:\n - value: 15 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000125\n alias: surf_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n suspend_part_matter:\n name: suspend_part_matter\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of suspended particulate matter\n title: suspended particulate matter\n examples:\n - value: 0.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - suspended particulate matter\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000741\n alias: suspend_part_matter\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n suspend_solids:\n name: suspend_solids\n annotations:\n expected_value:\n tag: expected_value\n value: suspended solid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, milligram per liter, mole per liter, gram per liter,\n part per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances including a wide variety of material,\n such as silt, decaying plant and animal matter; can include multiple substances\n title: suspended solids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - suspended solids\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000150\n alias: suspend_solids\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n tan:\n name: tan\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\n title: total acid number\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total acid number\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000120\n alias: tan\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n temp:\n name: temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n description: Temperature of the sample at the time of sampling.\n title: temperature\n examples:\n - value: 25 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - temperature\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000113\n alias: temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n temp_out:\n name: temp_out\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded temperature value at sampling time outside\n title: temperature outside house\n examples:\n - value: 5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - temperature outside house\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000197\n alias: temp_out\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tertiary_treatment:\n name: tertiary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: tertiary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process providing a final treatment stage to raise the effluent\n quality before it is discharged to the receiving environment\n title: tertiary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tertiary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000352\n alias: tertiary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n tidal_stage:\n name: tidal_stage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Stage of tide\n title: tidal stage\n examples:\n - value: high tide\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tidal stage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000750\n alias: tidal_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: tidal_stage_enum\n multivalued: false\n tillage:\n name: tillage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Note method(s) used for tilling\n title: history/tillage\n examples:\n - value: chisel\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/tillage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001081\n alias: tillage\n owner: Biosample\n domain_of:\n - Biosample\n range: tillage_enum\n multivalued: true\n tiss_cult_growth_med:\n name: tiss_cult_growth_med\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of plant tissue culture growth media used\n title: tissue culture growth media\n examples:\n - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tissue culture growth media\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001070\n alias: tiss_cult_growth_med\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n toluene:\n name: toluene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of toluene in the sample\n title: toluene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - toluene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000154\n alias: toluene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_carb:\n name: tot_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total carbon content\n title: total carbon\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000525\n alias: tot_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_depth_water_col:\n name: tot_depth_water_col\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of total depth of water column\n title: total depth of water column\n examples:\n - value: 500 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total depth of water column\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000634\n alias: tot_depth_water_col\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_diss_nitro:\n name: tot_diss_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\n title: total dissolved nitrogen\n examples:\n - value: 40 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total dissolved nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000744\n alias: tot_diss_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_inorg_nitro:\n name: tot_inorg_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total inorganic nitrogen content\n title: total inorganic nitrogen\n examples:\n - value: 40 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total inorganic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000745\n alias: tot_inorg_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_iron:\n name: tot_iron\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, milligram per kilogram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of total iron in the sample\n title: total iron\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total iron\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000105\n alias: tot_iron\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_nitro:\n name: tot_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total nitrogen concentration of water samples, calculated by: total\n nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n without filtering, reported as nitrogen'\n title: total nitrogen concentration\n examples:\n - value: 50 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total nitrogen concentration\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000102\n alias: tot_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the total nitrogen\n title: total nitrogen content method\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total nitrogen content method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000338\n alias: tot_nitro_cont_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n tot_nitro_content:\n name: tot_nitro_content\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total nitrogen content of the sample\n title: total nitrogen content\n examples:\n - value: 5 mg N/ L\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total nitrogen content\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000530\n alias: tot_nitro_content\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_org_c_meth:\n name: tot_org_c_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining total organic carbon\n title: total organic carbon method\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total organic carbon method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000337\n alias: tot_org_c_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n tot_org_carb:\n name: tot_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram Carbon per kilogram sample material\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Definition for soil: total organic carbon content of the soil, definition\n otherwise: total organic carbon content'\n title: total organic carbon\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000533\n alias: tot_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_part_carb:\n name: tot_part_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total particulate carbon content\n title: total particulate carbon\n examples:\n - value: 35 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total particulate carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000747\n alias: tot_part_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_phosp:\n name: tot_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total phosphorus concentration in the sample, calculated by: total\n phosphorus = total dissolved phosphorus + particulate phosphorus'\n title: total phosphorus\n examples:\n - value: 0.03 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000117\n alias: tot_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_phosphate:\n name: tot_phosphate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total amount or concentration of phosphate\n title: total phosphate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total phosphate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000689\n alias: tot_phosphate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_sulfur:\n name: tot_sulfur\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of total sulfur in the sample\n title: total sulfur\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total sulfur\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000419\n alias: tot_sulfur\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n train_line:\n name: train_line\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The subway line name\n title: train line\n examples:\n - value: red\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train line\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000837\n alias: train_line\n owner: Biosample\n domain_of:\n - Biosample\n range: train_line_enum\n multivalued: false\n train_stat_loc:\n name: train_stat_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The train station collection location\n title: train station collection location\n examples:\n - value: forest hills\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train station collection location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000838\n alias: train_stat_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: train_stat_loc_enum\n multivalued: false\n train_stop_loc:\n name: train_stop_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The train stop collection location\n title: train stop collection location\n examples:\n - value: end\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train stop collection location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000839\n alias: train_stop_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: train_stop_loc_enum\n multivalued: false\n turbidity:\n name: turbidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: formazin turbidity unit, formazin nephelometric units\n occurrence:\n tag: occurrence\n value: '1'\n description: Measure of the amount of cloudiness or haziness in water caused by\n individual particles\n title: turbidity\n examples:\n - value: 0.3 nephelometric turbidity units\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - turbidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000191\n alias: turbidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tvdss_of_hcr_press:\n name: tvdss_of_hcr_press\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original pressure was measured (e.g. 1578 m).\n title: depth (TVDSS) of hydrocarbon resource pressure\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth (TVDSS) of hydrocarbon resource pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000397\n alias: tvdss_of_hcr_press\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tvdss_of_hcr_temp:\n name: tvdss_of_hcr_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original temperature was measured (e.g. 1345 m).\n title: depth (TVDSS) of hydrocarbon resource temperature\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth (TVDSS) of hydrocarbon resource temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000394\n alias: tvdss_of_hcr_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n typ_occup_density:\n name: typ_occup_density\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Customary or normal density of occupants\n title: typical occupant density\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - typical occupant density\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000771\n alias: typ_occup_density\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n multivalued: false\n ventilation_rate:\n name: ventilation_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per minute, liters per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Ventilation rate of the system in the sampled premises\n title: ventilation rate\n examples:\n - value: 750 cubic meter per minute\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ventilation rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000114\n alias: ventilation_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ventilation_type:\n name: ventilation_type\n annotations:\n expected_value:\n tag: expected_value\n value: ventilation type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Ventilation system used in the sampled premises\n title: ventilation type\n examples:\n - value: Operable windows\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ventilation type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000756\n alias: ventilation_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n vfa:\n name: vfa\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of Volatile Fatty Acids in the sample\n title: volatile fatty acids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volatile fatty acids\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000152\n alias: vfa\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n vfa_fw:\n name: vfa_fw\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original volatile fatty acid concentration in the hydrocarbon resource\n title: vfa in formation water\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - vfa in formation water\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000408\n alias: vfa_fw\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n vis_media:\n name: vis_media\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building visual media\n title: visual media\n examples:\n - value: 3D scans\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - visual media\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000840\n alias: vis_media\n owner: Biosample\n domain_of:\n - Biosample\n range: vis_media_enum\n multivalued: false\n viscosity:\n name: viscosity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: cP at degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\n title: viscosity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - viscosity\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000126\n alias: viscosity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n volatile_org_comp:\n name: volatile_org_comp\n annotations:\n expected_value:\n tag: expected_value\n value: volatile organic compound name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per cubic meter, parts per million, nanogram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of carbon-based chemicals that easily evaporate at\n room temperature; can report multiple volatile organic compounds by entering\n numeric values preceded by name of compound\n title: volatile organic compounds\n examples:\n - value: formaldehyde;500 nanogram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volatile organic compounds\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000115\n alias: volatile_org_comp\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n wall_area:\n name: wall_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The total area of the sampled room's walls\n title: wall area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000198\n alias: wall_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n wall_const_type:\n name: wall_const_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building class of the wall defined by the composition of the\n building elements and fire-resistance rating.\n title: wall construction type\n examples:\n - value: fire resistive\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall construction type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000841\n alias: wall_const_type\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_const_type_enum\n multivalued: false\n wall_finish_mat:\n name: wall_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The material utilized to finish the outer most layer of the wall\n title: wall finish material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000842\n alias: wall_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_finish_mat_enum\n multivalued: false\n wall_height:\n name: wall_height\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average height of the walls in the sampled room\n title: wall height\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall height\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000221\n alias: wall_height\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n wall_loc:\n name: wall_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the wall within the room\n title: wall location\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000843\n alias: wall_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_loc_enum\n multivalued: false\n wall_surf_treatment:\n name: wall_surf_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The surface treatment of interior wall\n title: wall surface treatment\n examples:\n - value: paneling\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall surface treatment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000845\n alias: wall_surf_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_surf_treatment_enum\n multivalued: false\n wall_texture:\n name: wall_texture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The feel, appearance, or consistency of a wall surface\n title: wall texture\n examples:\n - value: popcorn\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall texture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000846\n alias: wall_texture\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_texture_enum\n multivalued: false\n wall_thermal_mass:\n name: wall_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the wall to provide inertia against temperature fluctuations.\n Generally this means concrete or concrete block that is either exposed or covered\n only with paint\n title: wall thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000222\n alias: wall_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n wall_water_mold:\n name: wall_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on a wall\n title: wall signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000844\n alias: wall_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n wastewater_type:\n name: wastewater_type\n annotations:\n expected_value:\n tag: expected_value\n value: wastewater type name\n occurrence:\n tag: occurrence\n value: '1'\n description: The origin of wastewater such as human waste, rainfall, storm drains,\n etc.\n title: wastewater type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wastewater type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000353\n alias: wastewater_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n water_cont_soil_meth:\n name: water_cont_soil_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the water content of soil\n title: water content method\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water content method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000323\n alias: water_cont_soil_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n description: Water content measurement\n title: water content\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water content\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000185\n alias: water_content\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n water_current:\n name: water_current\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per second, knots\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of magnitude and direction of flow within a fluid\n title: water current\n examples:\n - value: 10 cubic meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water current\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000203\n alias: water_current\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n water_cut:\n name: water_cut\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: Current amount of water (%) in a produced fluid stream; or the average\n of the combined streams\n title: water cut\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water cut\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000454\n alias: water_cut\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n water_feat_size:\n name: water_feat_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The size of the water feature\n title: water feature size\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water feature size\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000223\n alias: water_feat_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n water_feat_type:\n name: water_feat_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of water feature present within the building being sampled\n title: water feature type\n examples:\n - value: stream\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water feature type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000847\n alias: water_feat_type\n owner: Biosample\n domain_of:\n - Biosample\n range: water_feat_type_enum\n multivalued: false\n water_prod_rate:\n name: water_prod_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Water production rates per well (e.g. 987 m3 / day)\n title: water production rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water production rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000453\n alias: water_prod_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n water_temp_regm:\n name: water_temp_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to water with varying\n degree of temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple regimens\n title: water temperature regimen\n examples:\n - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water temperature regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000590\n alias: water_temp_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n watering_regm:\n name: watering_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milliliter, liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to watering frequencies,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple regimens\n title: watering regimen\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - watering regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000591\n alias: watering_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n weekday:\n name: weekday\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The day of the week when sampling occurred\n title: weekday\n examples:\n - value: Sunday\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weekday\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000848\n alias: weekday\n owner: Biosample\n domain_of:\n - Biosample\n range: weekday_enum\n multivalued: false\n win:\n name: win\n annotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\n description: 'A unique identifier of a well or wellbore. This is part of the Global\n Framework for Well Identification initiative which is compiled by the Professional\n Petroleum Data Management Association (PPDM) in an effort to improve well identification\n systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\n title: well identification number\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - well identification number\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000297\n alias: win\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n wind_direction:\n name: wind_direction\n annotations:\n expected_value:\n tag: expected_value\n value: wind direction name\n occurrence:\n tag: occurrence\n value: '1'\n description: Wind direction is the direction from which a wind originates\n title: wind direction\n examples:\n - value: Northwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wind direction\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000757\n alias: wind_direction\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n wind_speed:\n name: wind_speed\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second, kilometer per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Speed of wind measured at the time of sampling\n title: wind speed\n examples:\n - value: 21 kilometer per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wind speed\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000118\n alias: wind_speed\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n window_cond:\n name: window_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the window at the time of sampling\n title: window condition\n examples:\n - value: rupture\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000849\n alias: window_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: window_cond_enum\n multivalued: false\n window_cover:\n name: window_cover\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of window covering\n title: window covering\n examples:\n - value: curtains\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window covering\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000850\n alias: window_cover\n owner: Biosample\n domain_of:\n - Biosample\n range: window_cover_enum\n multivalued: false\n window_horiz_pos:\n name: window_horiz_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The horizontal position of the window on the wall\n title: window horizontal position\n examples:\n - value: middle\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window horizontal position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000851\n alias: window_horiz_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: window_horiz_pos_enum\n multivalued: false\n window_loc:\n name: window_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the window within the room\n title: window location\n examples:\n - value: west\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000852\n alias: window_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: window_loc_enum\n multivalued: false\n window_mat:\n name: window_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material used to finish a window\n title: window material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000853\n alias: window_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: window_mat_enum\n multivalued: false\n window_open_freq:\n name: window_open_freq\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times windows are opened per week\n title: window open frequency\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window open frequency\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000246\n alias: window_open_freq\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n window_size:\n name: window_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: inch, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The window's length and width\n title: window area/size\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window area/size\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit} x {float} {unit}'\n slot_uri: MIXS:0000224\n alias: window_size\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n window_status:\n name: window_status\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Defines whether the windows were open or closed during environmental\n testing\n title: window status\n examples:\n - value: open\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window status\n rank: 1000\n is_a: core field\n string_serialization: '[closed|open]'\n slot_uri: MIXS:0000855\n alias: window_status\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n window_type:\n name: window_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of windows\n title: window type\n examples:\n - value: fixed window\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000856\n alias: window_type\n owner: Biosample\n domain_of:\n - Biosample\n range: window_type_enum\n multivalued: false\n window_vert_pos:\n name: window_vert_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The vertical position of the window on the wall\n title: window vertical position\n examples:\n - value: middle\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window vertical position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000857\n alias: window_vert_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: window_vert_pos_enum\n multivalued: false\n window_water_mold:\n name: window_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the window.\n title: window signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000854\n alias: window_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n xylene:\n name: xylene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of xylene in the sample\n title: xylene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - xylene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000156\n alias: xylene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n zinc:\n name: zinc\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of zinc in the sample\n title: zinc\n examples:\n - value: 2.5 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - zinc\n rank: 1000\n alias: zinc\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: Biosample\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n community:\n name: community\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: community\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n habitat:\n name: habitat\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: habitat\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: string\n host_name:\n name: host_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: host_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n location:\n name: location\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: location\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: Biosample\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n ncbi_taxonomy_name:\n name: ncbi_taxonomy_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_taxonomy_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n proport_woa_temperature:\n name: proport_woa_temperature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: proport_woa_temperature\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n salinity_category:\n name: salinity_category\n description: 'Categorical description of the sample''s salinity. Examples: halophile,\n halotolerant, hypersaline, huryhaline'\n notes:\n - maps to gold:salinity\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-metadata/pull/297\n rank: 1000\n alias: salinity_category\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n sample_collection_site:\n name: sample_collection_site\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sample_collection_site\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n soluble_iron_micromol:\n name: soluble_iron_micromol\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: soluble_iron_micromol\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n subsurface_depth:\n name: subsurface_depth\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: subsurface_depth\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n dna_absorb1:\n name: dna_absorb1\n description: 260/280 measurement of DNA sample purity\n title: DNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n alias: dna_absorb1\n owner: Biosample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_absorb2:\n name: dna_absorb2\n description: 260/230 measurement of DNA sample purity\n title: DNA absorbance 260/230\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n is_a: biomaterial_purity\n alias: dna_absorb2\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_collect_site:\n name: dna_collect_site\n description: Provide information on the site your DNA sample was collected from\n title: DNA collection site\n examples:\n - value: untreated pond water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: dna_collect_site\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_concentration:\n name: dna_concentration\n title: DNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n alias: dna_concentration\n owner: Biosample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n dna_cont_type:\n name: dna_cont_type\n description: Tube or plate (96-well)\n title: DNA container type\n examples:\n - value: plate\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n alias: dna_cont_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: JgiContTypeEnum\n recommended: true\n dna_container_id:\n name: dna_container_id\n title: DNA container label\n comments:\n - Must be unique across all tubes and plates, and <20 characters. All samples\n in a plate should have the same plate label.\n examples:\n - value: Pond_MT_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{text < 20 characters}'\n alias: dna_container_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_dnase:\n name: dna_dnase\n title: DNase treatment DNA\n comments:\n - Note DNase treatment is required for all RNA samples.\n examples:\n - value: 'no'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 13\n alias: dna_dnase\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: YesNoEnum\n recommended: true\n dna_isolate_meth:\n name: dna_isolate_meth\n description: Describe the method/protocol/kit used to extract DNA/RNA.\n title: DNA isolation method\n examples:\n - value: phenol/chloroform extraction\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Sample Isolation Method\n rank: 16\n string_serialization: '{text}'\n alias: dna_isolate_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_organisms:\n name: dna_organisms\n description: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\n title: DNA expected organisms\n examples:\n - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n (1%)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{text}'\n alias: dna_organisms\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_project_contact:\n name: dna_project_contact\n title: DNA seq project contact\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: John Jones\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 18\n string_serialization: '{text}'\n alias: dna_project_contact\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_samp_id:\n name: dna_samp_id\n title: DNA sample ID\n todos:\n - Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n have two identifiers. How to force uniqueness? Moot because that column will\n be prefilled?\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '187654'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{text}'\n alias: dna_samp_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_sample_format:\n name: dna_sample_format\n description: Solution in which the DNA sample has been suspended\n title: DNA sample format\n examples:\n - value: Water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n alias: dna_sample_format\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: DNASampleFormatEnum\n recommended: true\n dna_sample_name:\n name: dna_sample_name\n description: Give the DNA sample a name that is meaningful to you. Sample names\n must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n title: DNA sample name\n examples:\n - value: JGI_pond_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{text}'\n alias: dna_sample_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project:\n name: dna_seq_project\n title: DNA seq project ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '1191234'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Seq Project ID\n rank: 1\n string_serialization: '{text}'\n alias: dna_seq_project\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project_pi:\n name: dna_seq_project_pi\n title: DNA seq project PI\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: Jane Johnson\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 17\n string_serialization: '{text}'\n alias: dna_seq_project_pi\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project_name:\n name: dna_seq_project_name\n title: DNA seq project name\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: JGI Pond metagenomics\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{text}'\n alias: dna_seq_project_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_volume:\n name: dna_volume\n title: DNA volume in ul\n comments:\n - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n form accepts values < 25, but JGI may refuse to process them unless permission\n has been granted by a project manager\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{float}'\n alias: dna_volume\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n proposal_dna:\n name: proposal_dna\n title: DNA proposal ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '504000'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 19\n string_serialization: '{text}'\n alias: proposal_dna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dnase_rna:\n name: dnase_rna\n title: DNase treated\n comments:\n - Note DNase treatment is required for all RNA samples.\n examples:\n - value: 'no'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Was Sample DNAse treated?\n rank: 13\n alias: dnase_rna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: YesNoEnum\n recommended: true\n proposal_rna:\n name: proposal_rna\n title: RNA proposal ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '504000'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 19\n string_serialization: '{text}'\n alias: proposal_rna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_absorb1:\n name: rna_absorb1\n description: 260/280 measurement of RNA sample purity\n title: RNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n string_serialization: '{float}'\n alias: rna_absorb1\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n rna_absorb2:\n name: rna_absorb2\n description: 260/230 measurement of RNA sample purity\n title: RNA absorbance 260/230\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n string_serialization: '{float}'\n alias: rna_absorb2\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n rna_collect_site:\n name: rna_collect_site\n description: Provide information on the site your RNA sample was collected from\n title: RNA collection site\n examples:\n - value: untreated pond water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: rna_collect_site\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_concentration:\n name: rna_concentration\n title: RNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n string_serialization: '{float}'\n alias: rna_concentration\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n rna_cont_type:\n name: rna_cont_type\n description: Tube or plate (96-well)\n title: RNA container type\n examples:\n - value: plate\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n alias: rna_cont_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: JgiContTypeEnum\n recommended: true\n rna_cont_well:\n name: rna_cont_well\n title: RNA plate position\n comments:\n - Required when 'plate' is selected for container type.\n - Leave blank if the sample will be shipped in a tube.\n - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n pass validation.\n - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n examples:\n - value: B2\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{96 well plate pos}'\n alias: rna_cont_well\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n rna_container_id:\n name: rna_container_id\n title: RNA container label\n comments:\n - Must be unique across all tubes and plates, and <20 characters. All samples\n in a plate should have the same plate label.\n examples:\n - value: Pond_MT_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{text < 20 characters}'\n alias: rna_container_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_isolate_meth:\n name: rna_isolate_meth\n description: Describe the method/protocol/kit used to extract DNA/RNA.\n title: RNA isolation method\n examples:\n - value: phenol/chloroform extraction\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Sample Isolation Method\n rank: 16\n string_serialization: '{text}'\n alias: rna_isolate_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_organisms:\n name: rna_organisms\n description: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\n title: RNA expected organisms\n examples:\n - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n (1%)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{text}'\n alias: rna_organisms\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_project_contact:\n name: rna_project_contact\n title: RNA seq project contact\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: John Jones\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 18\n string_serialization: '{text}'\n alias: rna_project_contact\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_samp_id:\n name: rna_samp_id\n title: RNA sample ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '187654'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{text}'\n alias: rna_samp_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_sample_format:\n name: rna_sample_format\n description: Solution in which the RNA sample has been suspended\n title: RNA sample format\n examples:\n - value: Water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n alias: rna_sample_format\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: RNASampleFormatEnum\n recommended: true\n rna_sample_name:\n name: rna_sample_name\n description: Give the RNA sample a name that is meaningful to you. Sample names\n must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n title: RNA sample name\n examples:\n - value: JGI_pond_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{text}'\n alias: rna_sample_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n rna_seq_project:\n name: rna_seq_project\n title: RNA seq project ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '1191234'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Seq Project ID\n rank: 1\n string_serialization: '{text}'\n alias: rna_seq_project\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_seq_project_pi:\n name: rna_seq_project_pi\n title: RNA seq project PI\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: Jane Johnson\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 17\n string_serialization: '{text}'\n alias: rna_seq_project_pi\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_seq_project_name:\n name: rna_seq_project_name\n title: RNA seq project name\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: JGI Pond metatranscriptomics\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{text}'\n alias: rna_seq_project_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_volume:\n name: rna_volume\n title: RNA volume in ul\n comments:\n - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n form accepts values < 25, but JGI may refuse to process them unless permission\n has been granted by a project manager\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{float}'\n alias: rna_volume\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n collection_date_inc:\n name: collection_date_inc\n description: Date the incubation was harvested/collected/ended. Only relevant\n for incubation samples.\n title: incubation collection date\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\n comments:\n - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n are all acceptable.\n examples:\n - value: '2021-04-15'\n - value: 2021-04\n - value: '2021'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 2\n string_serialization: '{date, arbitrary precision}'\n alias: collection_date_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n collection_time:\n name: collection_time\n description: The time of sampling, either as an instance (single point) or interval.\n title: collection time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: '13:33'\n - value: '13:33:55'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 1\n string_serialization: '{time, seconds optional}'\n alias: collection_time\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n collection_time_inc:\n name: collection_time_inc\n description: Time the incubation was harvested/collected/ended. Only relevant\n for incubation samples.\n title: incubation collection time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: '13:33'\n - value: '13:33:55'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 3\n string_serialization: '{time, seconds optional}'\n alias: collection_time_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n experimental_factor_other:\n name: experimental_factor_other\n description: Other details about your sample that you feel can't be accurately\n represented in the available columns.\n title: experimental factor- other\n comments:\n - This slot accepts open-ended text about your sample.\n - We recommend using key:value pairs.\n - Provided pairs will be considered for inclusion as future slots/terms in this\n data collection template.\n examples:\n - value: 'experimental treatment: value'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000008\n - MIXS:0000300\n rank: 7\n string_serialization: '{text}'\n alias: experimental_factor_other\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n filter_method:\n name: filter_method\n description: Type of filter used or how the sample was filtered\n title: filter method\n comments:\n - describe the filter or provide a catalog number and manufacturer\n examples:\n - value: C18\n - value: Basix PES, 13-100-106 FisherSci\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000765\n rank: 6\n string_serialization: '{text}'\n alias: filter_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n isotope_exposure:\n name: isotope_exposure\n description: List isotope exposure or addition applied to your sample.\n title: isotope exposure/addition\n todos:\n - Can we make the H218O correctly super and subscripted?\n comments:\n - This is required when your experimental design includes the use of isotopically\n labeled compounds\n examples:\n - value: 13C glucose\n - value: 18O water\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000751\n rank: 16\n alias: isotope_exposure\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n micro_biomass_c_meth:\n name: micro_biomass_c_meth\n description: Reference or method used in determining microbial biomass carbon\n title: microbial biomass carbon method\n todos:\n - How should we separate values? | or ;? lets be consistent\n comments:\n - required if \"microbial_biomass_c\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(87)90052-6\n - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000339\n rank: 11\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: micro_biomass_c_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n micro_biomass_n_meth:\n name: micro_biomass_n_meth\n description: Reference or method used in determining microbial biomass nitrogen\n title: microbial biomass nitrogen method\n comments:\n - required if \"microbial_biomass_n\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(87)90052-6\n - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000339\n rank: 13\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: micro_biomass_n_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n microbial_biomass_c:\n name: microbial_biomass_c\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer.\n title: microbial biomass carbon\n comments:\n - If you provide this, correction factors used for conversion to the final units\n and method are required\n examples:\n - value: 0.05 ug C/g dry soil\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000650\n rank: 10\n string_serialization: '{float} {unit}'\n alias: microbial_biomass_c\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n microbial_biomass_n:\n name: microbial_biomass_n\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer.\n title: microbial biomass nitrogen\n comments:\n - If you provide this, correction factors used for conversion to the final units\n and method are required\n examples:\n - value: 0.05 ug N/g dry soil\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000650\n rank: 12\n string_serialization: '{float} {unit}'\n alias: microbial_biomass_n\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n non_microb_biomass:\n name: non_microb_biomass\n description: Amount of biomass; should include the name for the part of biomass\n measured, e.g.insect, plant, total. Can include multiple measurements separated\n by ;\n title: non-microbial biomass\n examples:\n - value: insect 0.23 ug; plant 1g\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000174\n - MIXS:0000650\n rank: 8\n string_serialization: '{text};{float} {unit}'\n alias: non_microb_biomass\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n non_microb_biomass_method:\n name: non_microb_biomass_method\n description: Reference or method used in determining biomass\n title: non-microbial biomass method\n comments:\n - required if \"non-microbial biomass\" is provided\n examples:\n - value: https://doi.org/10.1038/s41467-021-26181-3\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000650\n rank: 9\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: non_microb_biomass_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n org_nitro_method:\n name: org_nitro_method\n description: Method used for obtaining organic nitrogen\n title: organic nitrogen method\n comments:\n - required if \"org_nitro\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(85)90144-0\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000338\n - MIXS:0000205\n rank: 14\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: org_nitro_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n other_treatment:\n name: other_treatment\n description: Other treatments applied to your samples that are not applicable\n to the provided fields\n title: other treatments\n notes:\n - Values entered here will be used to determine potential new slots.\n comments:\n - This is an open text field to provide any treatments that cannot be captured\n in the provided slots.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000300\n rank: 15\n string_serialization: '{text}'\n alias: other_treatment\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n start_date_inc:\n name: start_date_inc\n description: Date the incubation was started. Only relevant for incubation samples.\n title: incubation start date\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\n comments:\n - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n are all acceptable.\n examples:\n - value: '2021-04-15'\n - value: 2021-04\n - value: '2021'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 4\n string_serialization: '{date, arbitrary precision}'\n alias: start_date_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n start_time_inc:\n name: start_time_inc\n description: Time the incubation was started. Only relevant for incubation samples.\n title: incubation start time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: '13:33'\n - value: '13:33:55'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 5\n string_serialization: '{time, seconds optional}'\n alias: start_time_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n project_id:\n name: project_id\n description: Proposal IDs or names associated with dataset\n title: project ID\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{text}'\n alias: project_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n replicate_number:\n name: replicate_number\n description: If sending biological replicates, indicate the rep number here.\n title: replicate number\n comments:\n - This will guide staff in ensuring your samples are blocked & randomized correctly\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{integer}'\n alias: replicate_number\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n sample_shipped:\n name: sample_shipped\n description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n sample sent to EMSL.\n title: sample shipped amount\n comments:\n - This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\n examples:\n - value: 15 g\n - value: 100 uL\n - value: 5 mL\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{float} {unit}'\n alias: sample_shipped\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n sample_type:\n name: sample_type\n description: Type of sample being submitted\n title: sample type\n comments:\n - This can vary from 'environmental package' if the sample is an extraction.\n examples:\n - value: water extracted soil\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n alias: sample_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: SampleTypeEnum\n recommended: true\n technical_reps:\n name: technical_reps\n description: If sending technical replicates of the same sample, indicate the\n replicate count.\n title: number technical replicate\n comments:\n - This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{integer}'\n alias: technical_reps\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n analysis_type:\n name: analysis_type\n description: Select all the data types associated or available for this biosample\n title: analysis/data type\n examples:\n - value: metagenomics; metabolomics; metaproteomics\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIxS:investigation_type\n rank: 3\n alias: analysis_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: Sample ID\n range: AnalysisTypeEnum\n recommended: true\n multivalued: true\n sample_link:\n name: sample_link\n description: A unique identifier to assign parent-child, subsample, or sibling\n samples. This is relevant when a sample or other material was used to generate\n the new sample.\n title: sample linkage\n comments:\n - 'This field allows multiple entries separated by ; (Examples: Soil collected\n from the field will link with the soil used in an incubation. The soil a plant\n was grown in links to the plant sample. An original culture sample was transferred\n to a new vial and generated a new sample)'\n examples:\n - value: IGSN:DSJ0284\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{text}:{text}'\n alias: sample_link\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: Sample ID\n range: string\n recommended: true\n multivalued: true\n bulk_elect_conductivity:\n name: bulk_elect_conductivity\n description: Electrical conductivity is a measure of the ability to carry electric\n current, which is mostly dictated by the chemistry of and amount of water.\n title: bulk electrical conductivity\n comments:\n - Provide the value output of the field instrument.\n examples:\n - value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')\n description: The conductivity measurement was 0.017 millisiemens per centimeter.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bulk_elect_conductivity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n infiltrations:\n name: infiltrations\n description: The amount of time it takes to complete each infiltration activity\n examples:\n - value: '[''00:01:32'', ''00:00:53'']'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1\n aliases:\n - infiltration_1\n - infiltration_2\n rank: 1000\n list_elements_ordered: true\n alias: infiltrations\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Biosample\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Biosample\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Biosample\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A uriorcurie reference to an external database or resource that provides\n additional information or context about a specific entity at NMDC.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Biosample\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Biosample\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Biosample\nunique_keys:\n samp_name_unique_key:\n unique_key_name: samp_name_unique_key\n unique_key_slots:\n - samp_name\nrules:\n- preconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: dna_well_requires_plate\n- preconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n description: DNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: dna_plate_requires_well\n- preconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: rna_well_requires_plate\n- preconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n description: RNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: rna_plate_requires_well\n\nFunding-based, sample location-based, or experimental method-based defined categories
URI: BiosampleCategoryEnum
"},{"location":"BiosampleCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description LTER https://lternet.edu/ SIP None SFA https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance Science Focus Area projects funded through the Department of Energy Office of... FICUS https://jgi.doe.gov/user-programs/program-info/ficus-overview NEON https://www.neonscience.org"},{"location":"BiosampleCategoryEnum/#slots","title":"Slots","text":"Name Description biosample_categories"},{"location":"BiosampleCategoryEnum/#aliases","title":"Aliases","text":"name: BiosampleCategoryEnum\ndescription: Funding-based, sample location-based, or experimental method-based defined\n categories\nnotes:\n- Currently, these values can associated with biosamples via the biosample_categories\n slot\n- They might also be applicable to other classes\n- They are intended to enable metadata search and or filtering, for example in the\n NMDC data portal, https://data.microbiomedata.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- category tag\nrank: 1000\npermissible_values:\n LTER:\n text: LTER\n meaning: https://lternet.edu/\n title: National Science Foundation's Long Term Ecological Research Network\n SIP:\n text: SIP\n SFA:\n text: SFA\n description: Science Focus Area projects funded through the Department of Energy\n Office of Science Biological and Environmental Research Program\n meaning: https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance\n title: Department of Energy Office of Science Biological and Environmental Research\n Program Laboratory Science Focus Areas\n FICUS:\n text: FICUS\n meaning: https://jgi.doe.gov/user-programs/program-info/ficus-overview\n title: Facilities Integrating Collaborations for User Science\n NEON:\n text: NEON\n meaning: https://www.neonscience.org\n title: National Science Foundation's National Ecological Observatory Network\n\nURI: BioticRelationshipEnum
"},{"location":"BioticRelationshipEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description free living None parasite None commensal None symbiont None"},{"location":"BioticRelationshipEnum/#slots","title":"Slots","text":"Name Description biotic_relationship Description of relationship(s) between the subject organism and other organis..."},{"location":"BioticRelationshipEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BioticRelationshipEnum/#schema-source","title":"Schema Source","text":"name: biotic_relationship_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n free living:\n text: free living\n parasite:\n text: parasite\n commensal:\n text: commensal\n symbiont:\n text: symbiont\n\nA binary (true or false) value
URI: xsd:boolean
base: Bool
uri: xsd:boolean
repr: bool
URI: BuildDocsEnum
"},{"location":"BuildDocsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building information model None commissioning report None complaint logs None contract administration None cost estimate None janitorial schedules or logs None maintenance plans None schedule None sections None shop drawings None submittals None ventilation system None windows None"},{"location":"BuildDocsEnum/#slots","title":"Slots","text":"Name Description build_docs The building design, construction and operation documents"},{"location":"BuildDocsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildDocsEnum/#schema-source","title":"Schema Source","text":"name: build_docs_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n building information model:\n text: building information model\n commissioning report:\n text: commissioning report\n complaint logs:\n text: complaint logs\n contract administration:\n text: contract administration\n cost estimate:\n text: cost estimate\n janitorial schedules or logs:\n text: janitorial schedules or logs\n maintenance plans:\n text: maintenance plans\n schedule:\n text: schedule\n sections:\n text: sections\n shop drawings:\n text: shop drawings\n submittals:\n text: submittals\n ventilation system:\n text: ventilation system\n windows:\n text: windows\n\nURI: BuildOccupTypeEnum
"},{"location":"BuildOccupTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description office None market None restaurant None residence None school None residential None commercial None low rise None high rise None wood framed None health care None airport None sports complex None"},{"location":"BuildOccupTypeEnum/#slots","title":"Slots","text":"Name Description build_occup_type The primary function for which a building or discrete part of a building is i..."},{"location":"BuildOccupTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildOccupTypeEnum/#schema-source","title":"Schema Source","text":"name: build_occup_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n office:\n text: office\n market:\n text: market\n restaurant:\n text: restaurant\n residence:\n text: residence\n school:\n text: school\n residential:\n text: residential\n commercial:\n text: commercial\n low rise:\n text: low rise\n high rise:\n text: high rise\n wood framed:\n text: wood framed\n health care:\n text: health care\n airport:\n text: airport\n sports complex:\n text: sports complex\n\nURI: BuildingSettingEnum
"},{"location":"BuildingSettingEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description urban None suburban None exurban None rural None"},{"location":"BuildingSettingEnum/#slots","title":"Slots","text":"Name Description building_setting A location (geography) where a building is set"},{"location":"BuildingSettingEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildingSettingEnum/#schema-source","title":"Schema Source","text":"name: building_setting_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n urban:\n text: urban\n suburban:\n text: suburban\n exurban:\n text: exurban\n rural:\n text: rural\n\nAn integer value that corresponds to a size in bytes
URI: xsd:long
base: int
uri: xsd:long
A calibration object that is associated with a process.
URI: nmdc:CalibrationInformation
classDiagram\n class CalibrationInformation\n click CalibrationInformation href \"../CalibrationInformation\"\n InformationObject <|-- CalibrationInformation\n click InformationObject href \"../InformationObject\"\n\n\n\n CalibrationInformation : alternative_identifiers\n\n CalibrationInformation : calibration_object\n\n CalibrationInformation --> \"0..1\" DataObject : calibration_object\n click DataObject href \"../DataObject\"\n\n CalibrationInformation : calibration_standard\n\n CalibrationInformation --> \"0..1\" CalibrationStandardEnum : calibration_standard\n click CalibrationStandardEnum href \"../CalibrationStandardEnum\"\n\n CalibrationInformation : calibration_target\n\n CalibrationInformation --> \"1\" CalibrationTargetEnum : calibration_target\n click CalibrationTargetEnum href \"../CalibrationTargetEnum\"\n\n CalibrationInformation : description\n\n CalibrationInformation : id\n\n CalibrationInformation : internal_calibration\n\n CalibrationInformation : name\n\n CalibrationInformation : type\n\n\n\nname: CalibrationInformation\ndescription: A calibration object that is associated with a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- calibration_object\n- internal_calibration\n- calibration_target\n- calibration_standard\nslot_usage:\n internal_calibration:\n name: internal_calibration\n required: true\n calibration_target:\n name: calibration_target\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:CalibrationInformation\nrules:\n- preconditions:\n slot_conditions:\n calibration_target:\n name: calibration_target\n equals_string: retention_index\n postconditions:\n slot_conditions:\n calibration_standard:\n name: calibration_standard\n required: true\n description: If the calibration_target is retention_index, a calibration_standard\n is required.\n title: calibration_standard_if_rt\n- preconditions:\n slot_conditions:\n internal_calibration:\n name: internal_calibration\n id_prefixes:\n - 'False'\n postconditions:\n slot_conditions:\n calibration_object:\n name: calibration_object\n required: true\n description: If internal_calibration is false, a calibration_object is required.\n title: calibration_object_if_not_internal_calibration\n\nname: CalibrationInformation\ndescription: A calibration object that is associated with a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n internal_calibration:\n name: internal_calibration\n required: true\n calibration_target:\n name: calibration_target\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n calibration_object:\n name: calibration_object\n description: the file containing calibration data object\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: calibration_object\n owner: CalibrationInformation\n domain_of:\n - CalibrationInformation\n range: DataObject\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n internal_calibration:\n name: internal_calibration\n description: whether internal calibration was used, if false, external calibration\n was used\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: internal_calibration\n owner: CalibrationInformation\n domain_of:\n - CalibrationInformation\n range: boolean\n required: true\n calibration_target:\n name: calibration_target\n description: the target measurement of the calibration\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: calibration_target\n owner: CalibrationInformation\n domain_of:\n - CalibrationInformation\n range: CalibrationTargetEnum\n required: true\n calibration_standard:\n name: calibration_standard\n description: the reference standard(s) used for calibration\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: calibration_standard\n owner: CalibrationInformation\n domain_of:\n - CalibrationInformation\n range: CalibrationStandardEnum\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: CalibrationInformation\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: CalibrationInformation\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: CalibrationInformation\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: CalibrationInformation\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: CalibrationInformation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:CalibrationInformation\nrules:\n- preconditions:\n slot_conditions:\n calibration_target:\n name: calibration_target\n equals_string: retention_index\n postconditions:\n slot_conditions:\n calibration_standard:\n name: calibration_standard\n required: true\n description: If the calibration_target is retention_index, a calibration_standard\n is required.\n title: calibration_standard_if_rt\n- preconditions:\n slot_conditions:\n internal_calibration:\n name: internal_calibration\n id_prefixes:\n - 'False'\n postconditions:\n slot_conditions:\n calibration_object:\n name: calibration_object\n required: true\n description: If internal_calibration is false, a calibration_object is required.\n title: calibration_object_if_not_internal_calibration\n\nURI: CalibrationStandardEnum
"},{"location":"CalibrationStandardEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fames None alkanes None"},{"location":"CalibrationStandardEnum/#slots","title":"Slots","text":"Name Description calibration_standard the reference standard(s) used for calibration"},{"location":"CalibrationStandardEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationStandardEnum/#schema-source","title":"Schema Source","text":"name: CalibrationStandardEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n fames:\n text: fames\n aliases:\n - FAMES\n alkanes:\n text: alkanes\n aliases:\n - Alkanes\n\nURI: CalibrationTargetEnum
"},{"location":"CalibrationTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mass_charge_ratio None retention_time None retention_index None"},{"location":"CalibrationTargetEnum/#slots","title":"Slots","text":"Name Description calibration_target the target measurement of the calibration"},{"location":"CalibrationTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationTargetEnum/#schema-source","title":"Schema Source","text":"name: CalibrationTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n mass_charge_ratio:\n text: mass_charge_ratio\n title: m/z\n aliases:\n - Mass\n - m/z\n retention_time:\n text: retention_time\n aliases:\n - RT\n retention_index:\n text: retention_index\n aliases:\n - RI\n\nURI: CeilCondEnum
"},{"location":"CeilCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"CeilCondEnum/#slots","title":"Slots","text":"Name Description ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide..."},{"location":"CeilCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilCondEnum/#schema-source","title":"Schema Source","text":"name: ceil_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nURI: CeilFinishMatEnum
"},{"location":"CeilFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drywall None mineral fibre None tiles None PVC None plasterboard None metal None fiberglass None stucco None mineral wool/calcium silicate None wood None"},{"location":"CeilFinishMatEnum/#slots","title":"Slots","text":"Name Description ceil_finish_mat The type of material used to finish a ceiling"},{"location":"CeilFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilFinishMatEnum/#schema-source","title":"Schema Source","text":"name: ceil_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n drywall:\n text: drywall\n mineral fibre:\n text: mineral fibre\n tiles:\n text: tiles\n PVC:\n text: PVC\n plasterboard:\n text: plasterboard\n metal:\n text: metal\n fiberglass:\n text: fiberglass\n stucco:\n text: stucco\n mineral wool/calcium silicate:\n text: mineral wool/calcium silicate\n wood:\n text: wood\n\nURI: CeilTextureEnum
"},{"location":"CeilTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"CeilTextureEnum/#slots","title":"Slots","text":"Name Description ceil_texture The feel, appearance, or consistency of a ceiling surface"},{"location":"CeilTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTextureEnum/#schema-source","title":"Schema Source","text":"name: ceil_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crows feet:\n text: crows feet\n crows-foot stomp:\n text: crows-foot stomp\n double skip:\n text: double skip\n hawk and trowel:\n text: hawk and trowel\n knockdown:\n text: knockdown\n popcorn:\n text: popcorn\n orange peel:\n text: orange peel\n rosebud stomp:\n text: rosebud stomp\n Santa-Fe texture:\n text: Santa-Fe texture\n skip trowel:\n text: skip trowel\n smooth:\n text: smooth\n stomp knockdown:\n text: stomp knockdown\n swirl:\n text: swirl\n\nURI: CeilTypeEnum
"},{"location":"CeilTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cathedral None dropped None concave None barrel-shaped None coffered None cove None stretched None"},{"location":"CeilTypeEnum/#slots","title":"Slots","text":"Name Description ceil_type The type of ceiling according to the ceiling's appearance or construction"},{"location":"CeilTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTypeEnum/#schema-source","title":"Schema Source","text":"name: ceil_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cathedral:\n text: cathedral\n dropped:\n text: dropped\n concave:\n text: concave\n barrel-shaped:\n text: barrel-shaped\n coffered:\n text: coffered\n cove:\n text: cove\n stretched:\n text: stretched\n\nURI: ChemicalConversionCategoryEnum
"},{"location":"ChemicalConversionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description addition None substitution None acid_base None reduction_oxidation None combustion None decomposition None protease_cleavage OBI:0600056 an enzymatic cleavage which relies on an enzyme with protease activity to act..."},{"location":"ChemicalConversionCategoryEnum/#slots","title":"Slots","text":"Name Description chemical_conversion_category The type of chemical conversion process"},{"location":"ChemicalConversionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalConversionCategoryEnum/#schema-source","title":"Schema Source","text":"name: ChemicalConversionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n addition:\n text: addition\n substitution:\n text: substitution\n acid_base:\n text: acid_base\n reduction_oxidation:\n text: reduction_oxidation\n combustion:\n text: combustion\n decomposition:\n text: decomposition\n protease_cleavage:\n text: protease_cleavage\n description: an enzymatic cleavage which relies on an enzyme with protease activity\n to act on proteins and to produce polypeptides (protein fragments).\n meaning: OBI:0600056\n\nA process that results in the interconversion of chemical species by a reaction to transform the reagents into products.
__
URI: nmdc:ChemicalConversionProcess
classDiagram\n class ChemicalConversionProcess\n click ChemicalConversionProcess href \"../ChemicalConversionProcess\"\n MaterialProcessing <|-- ChemicalConversionProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n ChemicalConversionProcess : alternative_identifiers\n\n ChemicalConversionProcess : chemical_conversion_category\n\n ChemicalConversionProcess --> \"0..1\" ChemicalConversionCategoryEnum : chemical_conversion_category\n click ChemicalConversionCategoryEnum href \"../ChemicalConversionCategoryEnum\"\n\n ChemicalConversionProcess : description\n\n ChemicalConversionProcess : duration\n\n ChemicalConversionProcess --> \"0..1\" QuantityValue : duration\n click QuantityValue href \"../QuantityValue\"\n\n ChemicalConversionProcess : end_date\n\n ChemicalConversionProcess : has_failure_categorization\n\n ChemicalConversionProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ChemicalConversionProcess : has_input\n\n ChemicalConversionProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n ChemicalConversionProcess : has_output\n\n ChemicalConversionProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n ChemicalConversionProcess : id\n\n ChemicalConversionProcess : instrument_used\n\n ChemicalConversionProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n ChemicalConversionProcess : name\n\n ChemicalConversionProcess : processing_institution\n\n ChemicalConversionProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ChemicalConversionProcess : protocol_link\n\n ChemicalConversionProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ChemicalConversionProcess : qc_comment\n\n ChemicalConversionProcess : qc_status\n\n ChemicalConversionProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ChemicalConversionProcess : start_date\n\n ChemicalConversionProcess : substances_used\n\n ChemicalConversionProcess --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n ChemicalConversionProcess : substances_volume\n\n ChemicalConversionProcess --> \"0..1\" QuantityValue : substances_volume\n click QuantityValue href \"../QuantityValue\"\n\n ChemicalConversionProcess : temperature\n\n ChemicalConversionProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n ChemicalConversionProcess : type\n\n\n\nname: ChemicalConversionProcess\ndescription: 'A process that results in the interconversion of chemical species by\n a reaction to transform the reagents into products.\n\n '\ncomments:\n- The values of both has_reagents slot and has_input slot are considered the reagents\n of a chemical process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical reaction\nexact_mappings:\n- MISO:0000001\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- chemical_conversion_category\n- duration\n- temperature\n- substances_used\n- substances_volume\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ChemicalConversionProcess\n\nname: ChemicalConversionProcess\ndescription: 'A process that results in the interconversion of chemical species by\n a reaction to transform the reagents into products.\n\n '\ncomments:\n- The values of both has_reagents slot and has_input slot are considered the reagents\n of a chemical process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical reaction\nexact_mappings:\n- MISO:0000001\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n chemical_conversion_category:\n name: chemical_conversion_category\n description: The type of chemical conversion process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chemical_conversion_category\n owner: ChemicalConversionProcess\n domain_of:\n - ChemicalConversionProcess\n range: ChemicalConversionCategoryEnum\n duration:\n name: duration\n description: The elapsed time of an activity.\n examples:\n - value: JsonObj(has_numeric_value=2, has_unit='hours')\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: duration\n owner: ChemicalConversionProcess\n domain_of:\n - MixingProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: QuantityValue\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: ChemicalConversionProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n substances_used:\n name: substances_used\n description: The substances that are combined to enable a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: ChemicalConversionProcess\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n substances_volume:\n name: substances_volume\n description: The volume of the combined substances that was included in a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_volume\n owner: ChemicalConversionProcess\n domain_of:\n - ChemicalConversionProcess\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: ChemicalConversionProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ChemicalConversionProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChemicalConversionProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChemicalConversionProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ChemicalConversionProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ChemicalConversionProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ChemicalConversionProcess\n\nAn atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states. A chemical entity is a physical entity that pertains to chemistry or biochemistry.
URI: nmdc:ChemicalEntity
classDiagram\n class ChemicalEntity\n click ChemicalEntity href \"../ChemicalEntity\"\n OntologyClass <|-- ChemicalEntity\n click OntologyClass href \"../OntologyClass\"\n\n\n\n ChemicalEntity : alternative_identifiers\n\n ChemicalEntity : alternative_names\n\n ChemicalEntity : chemical_formula\n\n ChemicalEntity : definition\n\n ChemicalEntity : description\n\n ChemicalEntity : id\n\n ChemicalEntity : name\n\n ChemicalEntity : relations\n\n ChemicalEntity --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n ChemicalEntity : type\n\n\n\nInstances of this class should have identifiers with one of the following prefixes:
CHEBI
MS
HMDB
name: ChemicalEntity\nid_prefixes:\n- CHEBI\n- MS\n- HMDB\ndescription: An atom or molecule that can be represented with a chemical formula.\n Include lipids, glycans, natural products, drugs. There may be different terms for\n distinct acid-base forms, protonation states. A chemical entity is a physical entity\n that pertains to chemistry or biochemistry.\ndeprecated: true; as of Jan 2025, NMDC only needs a handful of chemicals and its use\n cases can be served via an enumeration rather than supporting a full class.\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nslots:\n- chemical_formula\nclass_uri: nmdc:ChemicalEntity\n\nname: ChemicalEntity\nid_prefixes:\n- CHEBI\n- MS\n- HMDB\ndescription: An atom or molecule that can be represented with a chemical formula.\n Include lipids, glycans, natural products, drugs. There may be different terms for\n distinct acid-base forms, protonation states. A chemical entity is a physical entity\n that pertains to chemistry or biochemistry.\ndeprecated: true; as of Jan 2025, NMDC only needs a handful of chemicals and its use\n cases can be served via an enumeration rather than supporting a full class.\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nattributes:\n chemical_formula:\n name: chemical_formula\n description: A generic grouping for molecular formulae and empirical formulae\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chemical_formula\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: ChemicalEntity\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: ChemicalEntity\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: ChemicalEntity\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ChemicalEntity\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChemicalEntity\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChemicalEntity\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ChemicalEntity\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ChemicalEntity\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ChemicalEntity\n\nURI: ChemicalEntityEnum
"},{"location":"ChemicalEntityEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description acetonitrile CHEBI:38472 alphaLP MS:1001303 A serine protease that hydrolyzes peptide bonds at the C-terminus of threonin... ammonium_acetate CHEBI:62947 ammonium_bicarbonate CHEBI:184335 Arg-C CHEBI:157791 A cysteine protease that hydrolyzes peptide, ester, and amide bonds at the C-... Asp-N MS:1001304 A zinc metalloendopeptidase that hydrolyzes peptide bonds at the N-terminus o... chloroform CHEBI:35255 chymotrypsin MS:1001306 A serine protease that hydrolyzes peptide bonds at the C-terminus of tryptoph... formic_acid CHEBI:30751 A carboxylic acid that is the simplest aliphatic carboxylic acid, comprising ... glucose CHEBI:17234 Generally considered the most abundant monosaccharide in nature Glu-C None A serine protease that hydrolyzes peptide and ester bonds at the C-terminus o... isopropyl_alcohol CHEBI:17824 Lys-C MS:1001309 A serine protease that hydrolyzes peptide, ester, and amide bonds at the C-te... Lys-N MS:1003093 A metalloendopeptidase that hydrolyzes peptide bonds at the C-terminus of lys... methanol CHEBI:17790 trypsin CHEBI:9765 A serine protease that hydrolyzes peptide bonds at the C-terminus of arginine... water CHEBI:15377 Any form of water used in an experiment including deionized water, distilled ..."},{"location":"ChemicalEntityEnum/#slots","title":"Slots","text":"Name Description known_as The substance from which a portion was taken"},{"location":"ChemicalEntityEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalEntityEnum/#schema-source","title":"Schema Source","text":"name: ChemicalEntityEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n acetonitrile:\n text: acetonitrile\n meaning: CHEBI:38472\n alphaLP:\n text: alphaLP\n description: A serine protease that hydrolyzes peptide bonds at the C-terminus\n of threonine, alanine, serine, and valine.\n meaning: MS:1001303\n ammonium_acetate:\n text: ammonium_acetate\n meaning: CHEBI:62947\n ammonium_bicarbonate:\n text: ammonium_bicarbonate\n meaning: CHEBI:184335\n Arg-C:\n text: Arg-C\n description: A cysteine protease that hydrolyzes peptide, ester, and amide bonds\n at the C-terminus of arginine and with lower efficiency, lysine.\n meaning: CHEBI:157791\n Asp-N:\n text: Asp-N\n description: A zinc metalloendopeptidase that hydrolyzes peptide bonds at the\n N-terminus of aspartic acid.\n meaning: MS:1001304\n chloroform:\n text: chloroform\n meaning: CHEBI:35255\n chymotrypsin:\n text: chymotrypsin\n description: A serine protease that hydrolyzes peptide bonds at the C-terminus\n of tryptophan, leucine, tyrosine, and phenylalanine.\n meaning: MS:1001306\n formic_acid:\n text: formic_acid\n description: A carboxylic acid that is the simplest aliphatic carboxylic acid,\n comprising a hydrogen atom joined to the methyl group of methanol.\n meaning: CHEBI:30751\n glucose:\n text: glucose\n description: Generally considered the most abundant monosaccharide in nature.\n meaning: CHEBI:17234\n Glu-C:\n text: Glu-C\n description: A serine protease that hydrolyzes peptide and ester bonds at the\n C-terminus of aspartic acid or glutamic acid.\n isopropyl_alcohol:\n text: isopropyl_alcohol\n meaning: CHEBI:17824\n Lys-C:\n text: Lys-C\n description: A serine protease that hydrolyzes peptide, ester, and amide bonds\n at the C-terminus of lysine.\n meaning: MS:1001309\n Lys-N:\n text: Lys-N\n description: A metalloendopeptidase that hydrolyzes peptide bonds at the C-terminus\n of lysine.\n meaning: MS:1003093\n methanol:\n text: methanol\n meaning: CHEBI:17790\n trypsin:\n text: trypsin\n description: A serine protease that hydrolyzes peptide bonds at the C-terminus\n of arginine and lysine.\n meaning: CHEBI:9765\n water:\n text: water\n description: Any form of water used in an experiment including deionized water,\n distilled water, and ultrapure water. Protocol or materials and methods should\n be consulted for exact type of water used in an experiment.\n meaning: CHEBI:15377\n\nURI: ChromatographicCategoryEnum
"},{"location":"ChromatographicCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description liquid_chromatography None gas_chromatography None solid_phase_extraction None"},{"location":"ChromatographicCategoryEnum/#slots","title":"Slots","text":"Name Description chromatographic_category The type of chromatography used in a process"},{"location":"ChromatographicCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChromatographicCategoryEnum/#schema-source","title":"Schema Source","text":"name: ChromatographicCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n liquid_chromatography:\n text: liquid_chromatography\n aliases:\n - LC\n gas_chromatography:\n text: gas_chromatography\n aliases:\n - GC\n solid_phase_extraction:\n text: solid_phase_extraction\n aliases:\n - SPE\n\nThe process of using a selective partitioning of the analyte or interferent between two immiscible phases.
URI: nmdc:ChromatographicSeparationProcess
classDiagram\n class ChromatographicSeparationProcess\n click ChromatographicSeparationProcess href \"../ChromatographicSeparationProcess\"\n MaterialProcessing <|-- ChromatographicSeparationProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n ChromatographicSeparationProcess : alternative_identifiers\n\n ChromatographicSeparationProcess : chromatographic_category\n\n ChromatographicSeparationProcess --> \"0..1\" ChromatographicCategoryEnum : chromatographic_category\n click ChromatographicCategoryEnum href \"../ChromatographicCategoryEnum\"\n\n ChromatographicSeparationProcess : description\n\n ChromatographicSeparationProcess : end_date\n\n ChromatographicSeparationProcess : has_failure_categorization\n\n ChromatographicSeparationProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ChromatographicSeparationProcess : has_input\n\n ChromatographicSeparationProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n ChromatographicSeparationProcess : has_output\n\n ChromatographicSeparationProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n ChromatographicSeparationProcess : id\n\n ChromatographicSeparationProcess : instrument_used\n\n ChromatographicSeparationProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n ChromatographicSeparationProcess : name\n\n ChromatographicSeparationProcess : ordered_mobile_phases\n\n ChromatographicSeparationProcess --> \"*\" MobilePhaseSegment : ordered_mobile_phases\n click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n ChromatographicSeparationProcess : processing_institution\n\n ChromatographicSeparationProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ChromatographicSeparationProcess : protocol_link\n\n ChromatographicSeparationProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ChromatographicSeparationProcess : qc_comment\n\n ChromatographicSeparationProcess : qc_status\n\n ChromatographicSeparationProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ChromatographicSeparationProcess : start_date\n\n ChromatographicSeparationProcess : stationary_phase\n\n ChromatographicSeparationProcess --> \"0..1\" StationaryPhaseEnum : stationary_phase\n click StationaryPhaseEnum href \"../StationaryPhaseEnum\"\n\n ChromatographicSeparationProcess : temperature\n\n ChromatographicSeparationProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n ChromatographicSeparationProcess : type\n\n\n\nname: ChromatographicSeparationProcess\ndescription: The process of using a selective partitioning of the analyte or interferent\n between two immiscible phases.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- chromatographic_category\n- ordered_mobile_phases\n- stationary_phase\n- temperature\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ChromatographicSeparationProcess\n\nname: ChromatographicSeparationProcess\ndescription: The process of using a selective partitioning of the analyte or interferent\n between two immiscible phases.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n chromatographic_category:\n name: chromatographic_category\n description: The type of chromatography used in a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chromatographic_category\n owner: ChromatographicSeparationProcess\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: ChromatographicCategoryEnum\n ordered_mobile_phases:\n name: ordered_mobile_phases\n description: The solution(s) that moves through a chromatography column.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n list_elements_ordered: true\n alias: ordered_mobile_phases\n owner: ChromatographicSeparationProcess\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: MobilePhaseSegment\n multivalued: true\n inlined: true\n inlined_as_list: true\n stationary_phase:\n name: stationary_phase\n description: The material the stationary phase is comprised of used in chromatography.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: stationary_phase\n owner: ChromatographicSeparationProcess\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: StationaryPhaseEnum\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: ChromatographicSeparationProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: ChromatographicSeparationProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ChromatographicSeparationProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChromatographicSeparationProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChromatographicSeparationProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ChromatographicSeparationProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ChromatographicSeparationProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ChromatographicSeparationProcess\n\nA set of parameters that define and control the actions of a chromatography process.
URI: nmdc:ChromatographyConfiguration
classDiagram\n class ChromatographyConfiguration\n click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n Configuration <|-- ChromatographyConfiguration\n click Configuration href \"../Configuration\"\n\n\n\n ChromatographyConfiguration : alternative_identifiers\n\n ChromatographyConfiguration : chromatographic_category\n\n ChromatographyConfiguration --> \"0..1\" ChromatographicCategoryEnum : chromatographic_category\n click ChromatographicCategoryEnum href \"../ChromatographicCategoryEnum\"\n\n ChromatographyConfiguration : description\n\n ChromatographyConfiguration : id\n\n ChromatographyConfiguration : name\n\n ChromatographyConfiguration : ordered_mobile_phases\n\n ChromatographyConfiguration --> \"*\" MobilePhaseSegment : ordered_mobile_phases\n click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n ChromatographyConfiguration : stationary_phase\n\n ChromatographyConfiguration --> \"0..1\" StationaryPhaseEnum : stationary_phase\n click StationaryPhaseEnum href \"../StationaryPhaseEnum\"\n\n ChromatographyConfiguration : temperature\n\n ChromatographyConfiguration --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n ChromatographyConfiguration : type\n\n\n\nname: ChromatographyConfiguration\ndescription: A set of parameters that define and control the actions of a chromatography\n process.\nnotes:\n- This class is intended to represent a chromatography method file associated with\n a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslots:\n- chromatographic_category\n- ordered_mobile_phases\n- stationary_phase\n- temperature\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ChromatographyConfiguration\n\nname: ChromatographyConfiguration\ndescription: A set of parameters that define and control the actions of a chromatography\n process.\nnotes:\n- This class is intended to represent a chromatography method file associated with\n a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n chromatographic_category:\n name: chromatographic_category\n description: The type of chromatography used in a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chromatographic_category\n owner: ChromatographyConfiguration\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: ChromatographicCategoryEnum\n ordered_mobile_phases:\n name: ordered_mobile_phases\n description: The solution(s) that moves through a chromatography column.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n list_elements_ordered: true\n alias: ordered_mobile_phases\n owner: ChromatographyConfiguration\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: MobilePhaseSegment\n multivalued: true\n inlined: true\n inlined_as_list: true\n stationary_phase:\n name: stationary_phase\n description: The material the stationary phase is comprised of used in chromatography.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: stationary_phase\n owner: ChromatographyConfiguration\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: StationaryPhaseEnum\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: ChromatographyConfiguration\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ChromatographyConfiguration\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChromatographyConfiguration\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n required: true\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChromatographyConfiguration\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n required: true\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ChromatographyConfiguration\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ChromatographyConfiguration\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ChromatographyConfiguration\n\nURI: nmdc:CollectingBiosamplesFromSite
classDiagram\n class CollectingBiosamplesFromSite\n click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n PlannedProcess <|-- CollectingBiosamplesFromSite\n click PlannedProcess href \"../PlannedProcess\"\n\n\n\n CollectingBiosamplesFromSite : alternative_identifiers\n\n CollectingBiosamplesFromSite : description\n\n CollectingBiosamplesFromSite : end_date\n\n CollectingBiosamplesFromSite : has_failure_categorization\n\n CollectingBiosamplesFromSite --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n CollectingBiosamplesFromSite : has_input\n\n CollectingBiosamplesFromSite --> \"1..*\" Site : has_input\n click Site href \"../Site\"\n\n CollectingBiosamplesFromSite : has_output\n\n CollectingBiosamplesFromSite --> \"1..*\" Biosample : has_output\n click Biosample href \"../Biosample\"\n\n CollectingBiosamplesFromSite : id\n\n CollectingBiosamplesFromSite : name\n\n CollectingBiosamplesFromSite : processing_institution\n\n CollectingBiosamplesFromSite --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n CollectingBiosamplesFromSite : protocol_link\n\n CollectingBiosamplesFromSite --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n CollectingBiosamplesFromSite : qc_comment\n\n CollectingBiosamplesFromSite : qc_status\n\n CollectingBiosamplesFromSite --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n CollectingBiosamplesFromSite : start_date\n\n CollectingBiosamplesFromSite : type\n\n\n\nname: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n has_input:\n name: has_input\n range: Site\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: Biosample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:CollectingBiosamplesFromSite\n\nname: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n has_input:\n name: has_input\n range: Site\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: Biosample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: Site\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: Biosample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: CollectingBiosamplesFromSite\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: CollectingBiosamplesFromSite\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: CollectingBiosamplesFromSite\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: CollectingBiosamplesFromSite\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:CollectingBiosamplesFromSite\n\nA set of parameters that define the actions of a process and is shared among multiple instances of the process.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:Configuration
classDiagram\n class Configuration\n click Configuration href \"../Configuration\"\n InformationObject <|-- Configuration\n click InformationObject href \"../InformationObject\"\n\n\n Configuration <|-- MassSpectrometryConfiguration\n click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n Configuration <|-- ChromatographyConfiguration\n click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n\n\n\n Configuration : alternative_identifiers\n\n Configuration : description\n\n Configuration : id\n\n Configuration : name\n\n Configuration : type\n\n\n\nname: Configuration\ndescription: A set of parameters that define the actions of a process and is shared\n among multiple instances of the process.\nnotes:\n- This class is intended to represent the parameters within a method file (or similar)\n that control a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nabstract: true\nclass_uri: nmdc:Configuration\n\nname: Configuration\ndescription: A set of parameters that define the actions of a process and is shared\n among multiple instances of the process.\nnotes:\n- This class is intended to represent the parameters within a method file (or similar)\n that control a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Configuration\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Configuration\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Configuration\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Configuration\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Configuration\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Configuration\n\nThe permitted types of containers used in processing metabolomic samples.
URI: ContainerCategoryEnum
"},{"location":"ContainerCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description v-bottom_conical_tube None falcon_tube None"},{"location":"ContainerCategoryEnum/#slots","title":"Slots","text":"Name Description contained_in A type of container"},{"location":"ContainerCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ContainerCategoryEnum/#schema-source","title":"Schema Source","text":"name: ContainerCategoryEnum\ndescription: The permitted types of containers used in processing metabolomic samples.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\npermissible_values:\n v-bottom_conical_tube:\n text: v-bottom_conical_tube\n falcon_tube:\n text: falcon_tube\n\nA controlled term or class from an ontology, requiring the presence of term with an id
URI: nmdc:ControlledIdentifiedTermValue
classDiagram\n class ControlledIdentifiedTermValue\n click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n ControlledTermValue <|-- ControlledIdentifiedTermValue\n click ControlledTermValue href \"../ControlledTermValue\"\n\n\n\n ControlledIdentifiedTermValue : has_raw_value\n\n ControlledIdentifiedTermValue : term\n\n ControlledIdentifiedTermValue --> \"1\" OntologyClass : term\n click OntologyClass href \"../OntologyClass\"\n\n ControlledIdentifiedTermValue : type\n\n\n\nname: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n term:\n name: term\n required: true\nclass_uri: nmdc:ControlledIdentifiedTermValue\n\nname: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n term:\n name: term\n required: true\nattributes:\n term:\n name: term\n description: pointer to an ontology class\n notes:\n - 'removed ''slot_uri: rdf:type'''\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: term\n owner: ControlledIdentifiedTermValue\n domain_of:\n - ControlledTermValue\n range: OntologyClass\n required: true\n inlined: true\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: ControlledIdentifiedTermValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ControlledIdentifiedTermValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ControlledIdentifiedTermValue\n\nA controlled term or class from an ontology
URI: nmdc:ControlledTermValue
classDiagram\n class ControlledTermValue\n click ControlledTermValue href \"../ControlledTermValue\"\n AttributeValue <|-- ControlledTermValue\n click AttributeValue href \"../AttributeValue\"\n\n\n ControlledTermValue <|-- ControlledIdentifiedTermValue\n click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n\n\n ControlledTermValue : has_raw_value\n\n ControlledTermValue : term\n\n ControlledTermValue --> \"0..1\" OntologyClass : term\n click OntologyClass href \"../OntologyClass\"\n\n ControlledTermValue : type\n\n\n\nname: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- term\nclass_uri: nmdc:ControlledTermValue\n\nname: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n term:\n name: term\n description: pointer to an ontology class\n notes:\n - 'removed ''slot_uri: rdf:type'''\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: term\n owner: ControlledTermValue\n domain_of:\n - ControlledTermValue\n range: OntologyClass\n inlined: true\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: ControlledTermValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ControlledTermValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ControlledTermValue\n\nThis class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role and for a person value. Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0
URI: prov:Association
classDiagram\n class CreditAssociation\n click CreditAssociation href \"../CreditAssociation\"\n\n CreditAssociation : applied_roles\n\n CreditAssociation --> \"1..*\" CreditEnum : applied_roles\n click CreditEnum href \"../CreditEnum\"\n\n CreditAssociation : applies_to_person\n\n CreditAssociation --> \"1\" PersonValue : applies_to_person\n click PersonValue href \"../PersonValue\"\n\n CreditAssociation : type\n\n\n\nname: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n will be at least a slot for a CRediT Contributor Role and for a person value. Specifically\n see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://casrai.org/credit/\naliases:\n- study role\n- credit table\n- associated researchers\nslots:\n- applies_to_person\n- applied_roles\n- type\nclass_uri: prov:Association\n\nname: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n will be at least a slot for a CRediT Contributor Role and for a person value. Specifically\n see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://casrai.org/credit/\naliases:\n- study role\n- credit table\n- associated researchers\nattributes:\n applies_to_person:\n name: applies_to_person\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: applies_to_person\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: PersonValue\n required: true\n applied_roles:\n name: applied_roles\n annotations:\n tooltip:\n tag: tooltip\n value: 'Identify all CRediT roles associated with this contributor. CRediT\n Information: https://info.orcid.org/credit-for-research-contribution ; CRediT:\n https://credit.niso.org/'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: applied_roles\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: CreditEnum\n required: true\n multivalued: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: CreditAssociation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: prov:Association\n\nURI: CreditEnum
"},{"location":"CreditEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Conceptualization None Conceptualization Data curation None Data curation Formal Analysis None Formal Analysis Funding acquisition None Funding acquisition Investigation None Investigation Methodology None Methodology Project administration None Project administration Resources None Resources Software None Software Supervision None Supervision Validation None Validation Visualization None Visualization Writing original draft None Writing \u2013 original draft Writing review and editing None Writing \u2013 review & editing Principal Investigator OBI:0000103 principal investigator role Submitter EFO:0001741 the person(s) who enter study and biosample metadata into the NMDC submission..."},{"location":"CreditEnum/#slots","title":"Slots","text":"Name Description applied_roles"},{"location":"CreditEnum/#comments","title":"Comments","text":"name: CreditEnum\ncomments:\n- CreditEnums come from https://casrai.org/credit/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Conceptualization:\n text: Conceptualization\n description: Conceptualization\n Data curation:\n text: Data curation\n description: Data curation\n Formal Analysis:\n text: Formal Analysis\n description: Formal Analysis\n Funding acquisition:\n text: Funding acquisition\n description: Funding acquisition\n Investigation:\n text: Investigation\n description: Investigation\n Methodology:\n text: Methodology\n description: Methodology\n Project administration:\n text: Project administration\n description: Project administration\n Resources:\n text: Resources\n description: Resources\n Software:\n text: Software\n description: Software\n Supervision:\n text: Supervision\n description: Supervision\n Validation:\n text: Validation\n description: Validation\n Visualization:\n text: Visualization\n description: Visualization\n Writing original draft:\n text: Writing original draft\n description: Writing \u2013 original draft\n Writing review and editing:\n text: Writing review and editing\n description: Writing \u2013 review & editing\n Principal Investigator:\n text: Principal Investigator\n description: principal investigator role\n meaning: OBI:0000103\n Submitter:\n text: Submitter\n description: the person(s) who enter study and biosample metadata into the NMDC\n submission portal\n meaning: EFO:0001741\n\nURI: CurLandUseEnum
"},{"location":"CurLandUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description badlands None cities None conifers None crop trees None farmstead None gravel None hardwoods None hayland None horticultural plants None industrial areas None intermixed hardwood and conifers None marshlands None meadows None mines/quarries None mudflats None oil waste areas None pastureland None permanent snow or ice None rainforest None rangeland None roads/railroads None rock None row crops None saline seeps None salt flats None sand None shrub crops None shrub land None small grains None successional shrub land None swamp None tropical None tundra None vegetable crops None vine crops None"},{"location":"CurLandUseEnum/#slots","title":"Slots","text":"Name Description cur_land_use Present state of sample site"},{"location":"CurLandUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CurLandUseEnum/#schema-source","title":"Schema Source","text":"name: cur_land_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n badlands:\n text: badlands\n cities:\n text: cities\n conifers:\n text: conifers\n annotations:\n originally:\n tag: originally\n value: conifers (e.g. pine,spruce,fir,cypress)\n examples:\n - value: cypress\n - value: fir\n - value: pine\n - value: spruce\n crop trees:\n text: crop trees\n annotations:\n originally:\n tag: originally\n value: crop trees (nuts,fruit,christmas trees,nursery trees)\n examples:\n - value: christmas trees\n - value: fruit\n - value: nursery trees\n - value: nuts\n farmstead:\n text: farmstead\n gravel:\n text: gravel\n hardwoods:\n text: hardwoods\n annotations:\n originally:\n tag: originally\n value: hardwoods (e.g. oak,hickory,elm,aspen)\n examples:\n - value: aspen\n - value: elm\n - value: hickory\n - value: oak\n hayland:\n text: hayland\n horticultural plants:\n text: horticultural plants\n annotations:\n originally:\n tag: originally\n value: horticultural plants (e.g. tulips)\n examples:\n - value: tulips\n industrial areas:\n text: industrial areas\n intermixed hardwood and conifers:\n text: intermixed hardwood and conifers\n marshlands:\n text: marshlands\n annotations:\n originally:\n tag: originally\n value: marshlands (grass,sedges,rushes)\n examples:\n - value: grass\n - value: rushes\n - value: sedgees\n meadows:\n text: meadows\n annotations:\n originally:\n tag: originally\n value: meadows (grasses,alfalfa,fescue,bromegrass,timothy)\n examples:\n - value: alfalfa\n - value: bromegrass\n - value: fescue\n - value: grasses\n - value: timothy\n mines/quarries:\n text: mines/quarries\n mudflats:\n text: mudflats\n oil waste areas:\n text: oil waste areas\n pastureland:\n text: pastureland\n annotations:\n originally:\n tag: originally\n value: pastureland (grasslands used for livestock grazing)\n comments:\n - grasslands used for livestock grazing\n permanent snow or ice:\n text: permanent snow or ice\n rainforest:\n text: rainforest\n annotations:\n originally:\n tag: originally\n value: rainforest (evergreen forest receiving greater than 406 cm annual rainfall)\n comments:\n - evergreen forest receiving greater than 406 cm annual rainfall\n rangeland:\n text: rangeland\n roads/railroads:\n text: roads/railroads\n rock:\n text: rock\n row crops:\n text: row crops\n saline seeps:\n text: saline seeps\n salt flats:\n text: salt flats\n sand:\n text: sand\n shrub crops:\n text: shrub crops\n annotations:\n originally:\n tag: originally\n value: shrub crops (blueberries,nursery ornamentals,filberts)\n examples:\n - value: blueberries\n - value: filberts\n - value: nursery ornamentals\n shrub land:\n text: shrub land\n annotations:\n originally:\n tag: originally\n value: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)\n examples:\n - value: creosote bush\n - value: eucalyptus\n - value: mesquite\n - value: sage-brush\n - value: shrub oak\n small grains:\n text: small grains\n successional shrub land:\n text: successional shrub land\n annotations:\n originally:\n tag: originally\n value: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub\n dogwoods,blackberries)\n examples:\n - value: blackberries\n - value: chokecherry\n - value: hazels\n - value: shrub dogwoods\n - value: sumacs\n - value: tree saplings\n swamp:\n text: swamp\n annotations:\n originally:\n tag: originally\n value: swamp (permanent or semi-permanent water body dominated by woody plants)\n comments:\n - permanent or semi-permanent water body dominated by woody plants\n tropical:\n text: tropical\n annotations:\n originally:\n tag: originally\n value: tropical (e.g. mangrove,palms)\n examples:\n - value: mangrove\n - value: palms\n tundra:\n text: tundra\n annotations:\n originally:\n tag: originally\n value: tundra (mosses,lichens)\n examples:\n - value: lichens\n - value: mosses\n vegetable crops:\n text: vegetable crops\n vine crops:\n text: vine crops\n annotations:\n originally:\n tag: originally\n value: vine crops (grapes)\n examples:\n - value: grapes\n\na compact URI
URI: xsd:string
base: Curie
uri: xsd:string
repr: str
URI: DNASampleFormatEnum
"},{"location":"DNASampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"DNASampleFormatEnum/#slots","title":"Slots","text":"Name Description dna_sample_format Solution in which the DNA sample has been suspended"},{"location":"DNASampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DNASampleFormatEnum/#schema-source","title":"Schema Source","text":"name: DNASampleFormatEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 10 mM Tris-HCl:\n text: 10 mM Tris-HCl\n DNAStable:\n text: DNAStable\n Ethanol:\n text: Ethanol\n Low EDTA TE:\n text: Low EDTA TE\n MDA reaction buffer:\n text: MDA reaction buffer\n PBS:\n text: PBS\n Pellet:\n text: Pellet\n RNAStable:\n text: RNAStable\n TE:\n text: TE\n Water:\n text: Water\n Gentegra-DNA:\n text: Gentegra-DNA\n Gentegra-RNA:\n text: Gentegra-RNA\n\nURI: DataCategoryEnum
"},{"location":"DataCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description instrument_data None Data generated by a DataGeneration PlannedProcess processed_data None Data generated by a WorkflowExecution PlannedProcess workflow_parameter_data None Data used as input into a workflow providing workflow specification"},{"location":"DataCategoryEnum/#slots","title":"Slots","text":"Name Description data_category The category of the file, such as instrument data from data generation or pro..."},{"location":"DataCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataCategoryEnum/#schema-source","title":"Schema Source","text":"name: DataCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n instrument_data:\n text: instrument_data\n description: Data generated by a DataGeneration PlannedProcess\n processed_data:\n text: processed_data\n description: Data generated by a WorkflowExecution PlannedProcess\n workflow_parameter_data:\n text: workflow_parameter_data\n description: Data used as input into a workflow providing workflow specification.\n related_mappings:\n - edam.data:0949\n\nThe methods and processes used to generate omics data from a biosample or organism.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:DataGeneration
classDiagram\n class DataGeneration\n click DataGeneration href \"../DataGeneration\"\n PlannedProcess <|-- DataGeneration\n click PlannedProcess href \"../PlannedProcess\"\n\n\n DataGeneration <|-- NucleotideSequencing\n click NucleotideSequencing href \"../NucleotideSequencing\"\n DataGeneration <|-- MassSpectrometry\n click MassSpectrometry href \"../MassSpectrometry\"\n\n\n\n DataGeneration : add_date\n\n DataGeneration : alternative_identifiers\n\n DataGeneration : analyte_category\n\n DataGeneration : associated_studies\n\n DataGeneration --> \"1..*\" Study : associated_studies\n click Study href \"../Study\"\n\n DataGeneration : description\n\n DataGeneration : end_date\n\n DataGeneration : has_failure_categorization\n\n DataGeneration --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n DataGeneration : has_input\n\n DataGeneration --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n DataGeneration : has_output\n\n DataGeneration --> \"*\" DataObject : has_output\n click DataObject href \"../DataObject\"\n\n DataGeneration : id\n\n DataGeneration : instrument_used\n\n DataGeneration --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n DataGeneration : mod_date\n\n DataGeneration : name\n\n DataGeneration : principal_investigator\n\n DataGeneration --> \"0..1\" PersonValue : principal_investigator\n click PersonValue href \"../PersonValue\"\n\n DataGeneration : processing_institution\n\n DataGeneration --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n DataGeneration : protocol_link\n\n DataGeneration --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n DataGeneration : qc_comment\n\n DataGeneration : qc_status\n\n DataGeneration --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n DataGeneration : start_date\n\n DataGeneration : type\n\n\n\nname: DataGeneration\ndescription: The methods and processes used to generate omics data from a biosample\n or organism.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An experiment contains information about a sequencing experiment\n including library and instrument details.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OmicsProcessing\n- assay\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nabstract: true\nslots:\n- add_date\n- analyte_category\n- associated_studies\n- instrument_used\n- mod_date\n- principal_investigator\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n associated_studies:\n name: associated_studies\n range: Study\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: DataObject\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:DataGeneration\n\nname: DataGeneration\ndescription: The methods and processes used to generate omics data from a biosample\n or organism.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An experiment contains information about a sequencing experiment\n including library and instrument details.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OmicsProcessing\n- assay\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n associated_studies:\n name: associated_studies\n range: Study\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: DataObject\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: DataGeneration\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n analyte_category:\n name: analyte_category\n description: \"The type of analyte(s) that were measured in the data generation\\\n \\ process and analyzed\\n in the Workflow Chain\\n\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: analyte_category\n owner: DataGeneration\n domain_of:\n - DataGeneration\n range: string\n required: true\n associated_studies:\n name: associated_studies\n description: The study associated with a resource.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: associated_studies\n owner: DataGeneration\n domain_of:\n - Biosample\n - DataGeneration\n range: Study\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: DataGeneration\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: DataGeneration\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n alias: principal_investigator\n owner: DataGeneration\n domain_of:\n - Study\n - DataGeneration\n range: PersonValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: DataObject\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: DataGeneration\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: DataGeneration\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: DataGeneration\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: DataGeneration\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: DataGeneration\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:DataGeneration\n\nAn object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.
URI: nmdc:DataObject
classDiagram\n class DataObject\n click DataObject href \"../DataObject\"\n InformationObject <|-- DataObject\n click InformationObject href \"../InformationObject\"\n\n\n\n DataObject : alternative_identifiers\n\n DataObject : compression_type\n\n DataObject : data_category\n\n DataObject --> \"0..1\" DataCategoryEnum : data_category\n click DataCategoryEnum href \"../DataCategoryEnum\"\n\n DataObject : data_object_type\n\n DataObject --> \"0..1\" FileTypeEnum : data_object_type\n click FileTypeEnum href \"../FileTypeEnum\"\n\n DataObject : description\n\n DataObject : file_size_bytes\n\n DataObject : id\n\n DataObject : in_manifest\n\n DataObject --> \"*\" Manifest : in_manifest\n click Manifest href \"../Manifest\"\n\n DataObject : insdc_experiment_identifiers\n\n DataObject : md5_checksum\n\n DataObject : name\n\n DataObject : type\n\n DataObject : url\n\n DataObject : was_generated_by\n\n DataObject --> \"0..1\" WorkflowExecution : was_generated_by\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\nname: DataObject\ndescription: An object that primarily consists of symbols that represent information. Files,\n records, and omics data are examples of data objects.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- compression_type\n- data_category\n- data_object_type\n- file_size_bytes\n- insdc_experiment_identifiers\n- md5_checksum\n- url\n- was_generated_by\n- in_manifest\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_generated_by:\n name: was_generated_by\n structured_pattern:\n syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n interpolated: true\nclass_uri: nmdc:DataObject\n\nname: DataObject\ndescription: An object that primarily consists of symbols that represent information. Files,\n records, and omics data are examples of data objects.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_generated_by:\n name: was_generated_by\n structured_pattern:\n syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n interpolated: true\nattributes:\n compression_type:\n name: compression_type\n description: If provided, specifies the compression type\n todos:\n - consider setting the range to an enum\n examples:\n - value: gzip\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: compression_type\n owner: DataObject\n domain_of:\n - DataObject\n range: string\n data_category:\n name: data_category\n description: The category of the file, such as instrument data from data generation\n or processed data from a workflow execution.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: data_category\n owner: DataObject\n domain_of:\n - DataObject\n range: DataCategoryEnum\n data_object_type:\n name: data_object_type\n description: The type of file represented by the data object.\n examples:\n - value: FT ICR-MS Analysis Results\n - value: GC-MS Metabolomics Results\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n data_object_type:\n literal_form: data_object_type\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n alias: data_object_type\n owner: DataObject\n domain_of:\n - DataObject\n range: FileTypeEnum\n file_size_bytes:\n name: file_size_bytes\n description: Size of the file in bytes\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: file_size_bytes\n owner: DataObject\n domain_of:\n - DataObject\n range: bytes\n insdc_experiment_identifiers:\n name: insdc_experiment_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_experiment_identifiers\n owner: DataObject\n domain_of:\n - NucleotideSequencing\n - DataObject\n range: external_identifier\n multivalued: true\n pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n md5_checksum:\n name: md5_checksum\n description: MD5 checksum of file (pre-compressed)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: md5_checksum\n owner: DataObject\n domain_of:\n - DataObject\n range: string\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: url\n owner: DataObject\n domain_of:\n - ImageValue\n - Protocol\n - DataObject\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: DataObject\n domain_of:\n - FunctionalAnnotationAggMember\n - FunctionalAnnotation\n - DataObject\n range: WorkflowExecution\n structured_pattern:\n syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n interpolated: true\n any_of:\n - range: WorkflowExecution\n - range: DataGeneration\n in_manifest:\n name: in_manifest\n description: one or more combinations of other DataObjects that can be analyzed\n together\n comments:\n - A DataObject can be part of multiple manifests, for example, a DataObject could\n be part of a manifest for a single run of an instrument and a manifest for technical\n replicates of a single sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: in_manifest\n owner: DataObject\n domain_of:\n - DataObject\n range: Manifest\n multivalued: true\n structured_pattern:\n syntax: ^{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$\n interpolated: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: DataObject\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: DataObject\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n required: true\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: DataObject\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n required: true\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: DataObject\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: DataObject\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:DataObject\n\nAn abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to collections.
URI: nmdc:Database
classDiagram\n class Database\n click Database href \"../Database\"\n\n Database : biosample_set\n\n Database --> \"*\" Biosample : biosample_set\n click Biosample href \"../Biosample\"\n\n Database : calibration_set\n\n Database --> \"*\" CalibrationInformation : calibration_set\n click CalibrationInformation href \"../CalibrationInformation\"\n\n Database : collecting_biosamples_from_site_set\n\n Database --> \"*\" CollectingBiosamplesFromSite : collecting_biosamples_from_site_set\n click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n\n Database : configuration_set\n\n Database --> \"*\" Configuration : configuration_set\n click Configuration href \"../Configuration\"\n\n Database : data_generation_set\n\n Database --> \"*\" DataGeneration : data_generation_set\n click DataGeneration href \"../DataGeneration\"\n\n Database : data_object_set\n\n Database --> \"*\" DataObject : data_object_set\n click DataObject href \"../DataObject\"\n\n Database : field_research_site_set\n\n Database --> \"*\" FieldResearchSite : field_research_site_set\n click FieldResearchSite href \"../FieldResearchSite\"\n\n Database : functional_annotation_agg\n\n Database --> \"*\" FunctionalAnnotationAggMember : functional_annotation_agg\n click FunctionalAnnotationAggMember href \"../FunctionalAnnotationAggMember\"\n\n Database : functional_annotation_set\n\n Database --> \"*\" FunctionalAnnotation : functional_annotation_set\n click FunctionalAnnotation href \"../FunctionalAnnotation\"\n\n Database : genome_feature_set\n\n Database --> \"*\" GenomeFeature : genome_feature_set\n click GenomeFeature href \"../GenomeFeature\"\n\n Database : instrument_set\n\n Database --> \"*\" Instrument : instrument_set\n click Instrument href \"../Instrument\"\n\n Database : manifest_set\n\n Database --> \"*\" Manifest : manifest_set\n click Manifest href \"../Manifest\"\n\n Database : material_processing_set\n\n Database --> \"*\" MaterialProcessing : material_processing_set\n click MaterialProcessing href \"../MaterialProcessing\"\n\n Database : processed_sample_set\n\n Database --> \"*\" ProcessedSample : processed_sample_set\n click ProcessedSample href \"../ProcessedSample\"\n\n Database : protocol_execution_set\n\n Database --> \"*\" ProtocolExecution : protocol_execution_set\n click ProtocolExecution href \"../ProtocolExecution\"\n\n Database : storage_process_set\n\n Database --> \"*\" StorageProcess : storage_process_set\n click StorageProcess href \"../StorageProcess\"\n\n Database : study_set\n\n Database --> \"*\" Study : study_set\n click Study href \"../Study\"\n\n Database : workflow_execution_set\n\n Database --> \"*\" WorkflowExecution : workflow_execution_set\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\nname: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n to correspond to an actual managed database top level holder class. When translated\n to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n of interest. For MongoDB, the lists of objects that Database slots point to correspond\n to **collections**.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nslots:\n- biosample_set\n- calibration_set\n- collecting_biosamples_from_site_set\n- configuration_set\n- data_generation_set\n- data_object_set\n- field_research_site_set\n- functional_annotation_agg\n- functional_annotation_set\n- genome_feature_set\n- instrument_set\n- manifest_set\n- material_processing_set\n- processed_sample_set\n- protocol_execution_set\n- storage_process_set\n- study_set\n- workflow_execution_set\nclass_uri: nmdc:Database\ntree_root: true\n\nname: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n to correspond to an actual managed database top level holder class. When translated\n to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n of interest. For MongoDB, the lists of objects that Database slots point to correspond\n to **collections**.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nattributes:\n biosample_set:\n name: biosample_set\n description: This property links a database object to the set of samples within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: biosample_set\n owner: Database\n domain_of:\n - Database\n range: Biosample\n multivalued: true\n inlined_as_list: true\n calibration_set:\n name: calibration_set\n description: This property links a database object to the set of calibrations\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: calibration_set\n owner: Database\n domain_of:\n - Database\n range: CalibrationInformation\n multivalued: true\n inlined_as_list: true\n collecting_biosamples_from_site_set:\n name: collecting_biosamples_from_site_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: collecting_biosamples_from_site_set\n owner: Database\n domain_of:\n - Database\n range: CollectingBiosamplesFromSite\n multivalued: true\n inlined_as_list: true\n configuration_set:\n name: configuration_set\n description: This property links a database object to the set of configurations\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: configuration_set\n owner: Database\n domain_of:\n - Database\n range: Configuration\n multivalued: true\n inlined_as_list: true\n data_generation_set:\n name: data_generation_set\n description: This property links a database object to the set of data generations\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: data_generation_set\n owner: Database\n domain_of:\n - Database\n range: DataGeneration\n multivalued: true\n inlined_as_list: true\n data_object_set:\n name: data_object_set\n description: This property links a database object to the set of data objects\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: data_object_set\n owner: Database\n domain_of:\n - Database\n range: DataObject\n multivalued: true\n inlined_as_list: true\n field_research_site_set:\n name: field_research_site_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: field_research_site_set\n owner: Database\n domain_of:\n - Database\n range: FieldResearchSite\n multivalued: true\n inlined_as_list: true\n functional_annotation_agg:\n name: functional_annotation_agg\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: functional_annotation_agg\n owner: Database\n domain_of:\n - Database\n range: FunctionalAnnotationAggMember\n multivalued: true\n inlined: true\n inlined_as_list: true\n functional_annotation_set:\n name: functional_annotation_set\n description: This property links a database object to the set of all functional\n annotations\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: functional_annotation_set\n owner: Database\n domain_of:\n - Database\n range: FunctionalAnnotation\n multivalued: true\n inlined_as_list: true\n genome_feature_set:\n name: genome_feature_set\n description: This property links a database object to the set of all features\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: genome_feature_set\n owner: Database\n domain_of:\n - Database\n range: GenomeFeature\n multivalued: true\n inlined_as_list: true\n instrument_set:\n name: instrument_set\n description: This property links a database object to the set of instruments within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: instrument_set\n owner: Database\n domain_of:\n - Database\n range: Instrument\n multivalued: true\n inlined_as_list: true\n manifest_set:\n name: manifest_set\n description: This property links a database object to the set of manifests within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: manifest_set\n owner: Database\n domain_of:\n - Database\n range: Manifest\n multivalued: true\n inlined_as_list: true\n material_processing_set:\n name: material_processing_set\n description: This property links a database object to the set of material processing\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: material_processing_set\n owner: Database\n domain_of:\n - Database\n range: MaterialProcessing\n multivalued: true\n inlined_as_list: true\n processed_sample_set:\n name: processed_sample_set\n description: This property links a database object to the set of processed samples\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: processed_sample_set\n owner: Database\n domain_of:\n - Database\n range: ProcessedSample\n multivalued: true\n inlined_as_list: true\n protocol_execution_set:\n name: protocol_execution_set\n description: This property links a database object to the set of protocol executions\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: protocol_execution_set\n owner: Database\n domain_of:\n - Database\n range: ProtocolExecution\n multivalued: true\n inlined_as_list: true\n storage_process_set:\n name: storage_process_set\n description: This property links a database object to the set of storage processes\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: storage_process_set\n owner: Database\n domain_of:\n - Database\n range: StorageProcess\n multivalued: true\n inlined_as_list: true\n study_set:\n name: study_set\n description: This property links a database object to the set of studies within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: study_set\n owner: Database\n domain_of:\n - Database\n range: Study\n multivalued: true\n inlined_as_list: true\n workflow_execution_set:\n name: workflow_execution_set\n description: This property links a database object to the set of workflow executions.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: workflow_execution_set\n owner: Database\n domain_of:\n - Database\n range: WorkflowExecution\n multivalued: true\n inlined_as_list: true\nclass_uri: nmdc:Database\ntree_root: true\n\na date (year, month and day) in an idealized calendar
URI: xsd:date
base: XSDDate
uri: xsd:date
repr: str
Either a date or a datetime
URI: linkml:DateOrDatetime
base: str
uri: linkml:DateOrDatetime
repr: str
The combination of a date and time
URI: xsd:dateTime
base: XSDDateTime
uri: xsd:dateTime
repr: str
A real number with arbitrary precision that conforms to the xsd:decimal specification
URI: xsd:decimal
base: Decimal
uri: xsd:decimal
A decimal degree expresses latitude or longitude as decimal fractions.
URI: xsd:decimal
base: float
uri: xsd:decimal
URI: DeposEnvEnum
"},{"location":"DeposEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Continental - Alluvial None Continental - Aeolian None Continental - Fluvial None Continental - Lacustrine None Transitional - Deltaic None Transitional - Tidal None Transitional - Lagoonal None Transitional - Beach None Transitional - Lake None Marine - Shallow None Marine - Deep None Marine - Reef None Other - Evaporite None Other - Glacial None Other - Volcanic None other None"},{"location":"DeposEnvEnum/#slots","title":"Slots","text":"Name Description depos_env Main depositional environment (https://en"},{"location":"DeposEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DeposEnvEnum/#schema-source","title":"Schema Source","text":"name: depos_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Continental - Alluvial:\n text: Continental - Alluvial\n Continental - Aeolian:\n text: Continental - Aeolian\n Continental - Fluvial:\n text: Continental - Fluvial\n Continental - Lacustrine:\n text: Continental - Lacustrine\n Transitional - Deltaic:\n text: Transitional - Deltaic\n Transitional - Tidal:\n text: Transitional - Tidal\n Transitional - Lagoonal:\n text: Transitional - Lagoonal\n Transitional - Beach:\n text: Transitional - Beach\n Transitional - Lake:\n text: Transitional - Lake\n Marine - Shallow:\n text: Marine - Shallow\n Marine - Deep:\n text: Marine - Deep\n Marine - Reef:\n text: Marine - Reef\n Other - Evaporite:\n text: Other - Evaporite\n Other - Glacial:\n text: Other - Glacial\n Other - Volcanic:\n text: Other - Volcanic\n other:\n text: other\n\nA mixing step where a soluble component is mixed with a liquid component.
__
URI: nmdc:DissolvingProcess
classDiagram\n class DissolvingProcess\n click DissolvingProcess href \"../DissolvingProcess\"\n MaterialProcessing <|-- DissolvingProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n DissolvingProcess : alternative_identifiers\n\n DissolvingProcess : description\n\n DissolvingProcess : duration\n\n DissolvingProcess --> \"0..1\" QuantityValue : duration\n click QuantityValue href \"../QuantityValue\"\n\n DissolvingProcess : end_date\n\n DissolvingProcess : has_failure_categorization\n\n DissolvingProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n DissolvingProcess : has_input\n\n DissolvingProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n DissolvingProcess : has_output\n\n DissolvingProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n DissolvingProcess : id\n\n DissolvingProcess : instrument_used\n\n DissolvingProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n DissolvingProcess : name\n\n DissolvingProcess : processing_institution\n\n DissolvingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n DissolvingProcess : protocol_link\n\n DissolvingProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n DissolvingProcess : qc_comment\n\n DissolvingProcess : qc_status\n\n DissolvingProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n DissolvingProcess : start_date\n\n DissolvingProcess : substances_used\n\n DissolvingProcess --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n DissolvingProcess : temperature\n\n DissolvingProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n DissolvingProcess : type\n\n\n\nname: DissolvingProcess\ndescription: 'A mixing step where a soluble component is mixed with a liquid component.\n\n '\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Solubilization\nexact_mappings:\n- CHMO:0002773\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- duration\n- temperature\n- substances_used\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:DissolvingProcess\n\nname: DissolvingProcess\ndescription: 'A mixing step where a soluble component is mixed with a liquid component.\n\n '\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Solubilization\nexact_mappings:\n- CHMO:0002773\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n duration:\n name: duration\n description: The elapsed time of an activity.\n examples:\n - value: JsonObj(has_numeric_value=2, has_unit='hours')\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: duration\n owner: DissolvingProcess\n domain_of:\n - MixingProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: QuantityValue\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: DissolvingProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n substances_used:\n name: substances_used\n description: The substances that are combined to enable a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: DissolvingProcess\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: DissolvingProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: DissolvingProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: DissolvingProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: DissolvingProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: DissolvingProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: DissolvingProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:DissolvingProcess\n\nA centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.
URI: nmdc:Doi
classDiagram\n class Doi\n click Doi href \"../Doi\"\n\n Doi : doi_category\n\n Doi --> \"1\" DoiCategoryEnum : doi_category\n click DoiCategoryEnum href \"../DoiCategoryEnum\"\n\n Doi : doi_provider\n\n Doi --> \"0..1\" DoiProviderEnum : doi_provider\n click DoiProviderEnum href \"../DoiProviderEnum\"\n\n Doi : doi_value\n\n Doi : type\n\n\n\nname: Doi\ndescription: A centrally registered identifier symbol used to uniquely identify objects\n given by the International DOI Foundation. The DOI system is particularly used for\n electronic documents.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOIs\n- digital object identifiers\nexact_mappings:\n- OBI:0002110\nslots:\n- doi_value\n- doi_provider\n- doi_category\n- type\nclass_uri: nmdc:Doi\nrules:\n- preconditions:\n slot_conditions:\n doi_category:\n name: doi_category\n any_of:\n - equals_string: dataset_doi\n - equals_string: award_doi\n postconditions:\n slot_conditions:\n doi_provider:\n name: doi_provider\n required: true\n description: If doi_category is a publication_doi, then doi_provider is not required.\n Otherwise, doi_provider is required.\n title: dataset_award_dois_required\n\nname: Doi\ndescription: A centrally registered identifier symbol used to uniquely identify objects\n given by the International DOI Foundation. The DOI system is particularly used for\n electronic documents.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOIs\n- digital object identifiers\nexact_mappings:\n- OBI:0002110\nattributes:\n doi_value:\n name: doi_value\n description: A digital object identifier, which is intended to persistantly identify\n some resource on the web.\n examples:\n - value: doi:10.46936/10.25585/60000880\n description: The DOI links to an electronic document.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - DOI\n - digital object identifier\n exact_mappings:\n - OBI:0002110\n narrow_mappings:\n - edam.data:1188\n rank: 1000\n alias: doi_value\n owner: Doi\n domain_of:\n - Doi\n range: uriorcurie\n required: true\n pattern: ^doi:10.\\d{2,9}/.*$\n doi_provider:\n name: doi_provider\n description: The authority, or organization, the DOI is associated with.\n examples:\n - value: ess_dive\n description: The corresponding DOI is associated with ESS-DIVE.\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - NCIT:C74932\n rank: 1000\n alias: doi_provider\n owner: Doi\n domain_of:\n - Doi\n range: DoiProviderEnum\n doi_category:\n name: doi_category\n description: The resource type the corresponding doi resolves to.\n examples:\n - value: dataset_doi\n description: The corresponding DOI is a dataset resource type.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: doi_category\n owner: Doi\n domain_of:\n - Doi\n range: DoiCategoryEnum\n required: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Doi\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Doi\nrules:\n- preconditions:\n slot_conditions:\n doi_category:\n name: doi_category\n any_of:\n - equals_string: dataset_doi\n - equals_string: award_doi\n postconditions:\n slot_conditions:\n doi_provider:\n name: doi_provider\n required: true\n description: If doi_category is a publication_doi, then doi_provider is not required.\n Otherwise, doi_provider is required.\n title: dataset_award_dois_required\n\nURI: DoiCategoryEnum
"},{"location":"DoiCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description award_doi None A type of DOI that resolves to a funding authority dataset_doi None A type of DOI that resolves to generated data publication_doi None A type of DOI that resolves to a publication data_management_plan_doi None A type of DOI that resolves to a data management plan"},{"location":"DoiCategoryEnum/#slots","title":"Slots","text":"Name Description doi_category The resource type the corresponding doi resolves to"},{"location":"DoiCategoryEnum/#comments","title":"Comments","text":"name: DoiCategoryEnum\ncomments:\n- See especially the resourceTypeGeneral section of the DataCite PDF, on pp48-53 as\n of 2023-07-19\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://schema.datacite.org/meta/kernel-4.4/doc/DataCite-MetadataKernel_v4.4.pdf\n- https://api.crossref.org/types\nrank: 1000\npermissible_values:\n award_doi:\n text: award_doi\n description: A type of DOI that resolves to a funding authority.\n dataset_doi:\n text: dataset_doi\n description: A type of DOI that resolves to generated data.\n publication_doi:\n text: publication_doi\n description: A type of DOI that resolves to a publication.\n data_management_plan_doi:\n text: data_management_plan_doi\n description: A type of DOI that resolves to a data management plan.\n\nURI: DoiProviderEnum
"},{"location":"DoiProviderEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description emsl https://ror.org/04rc0xn13 jgi https://ror.org/04xm1d337 kbase https://ror.org/01znn6x10 osti https://ror.org/031478740 ess_dive https://ror.org/01t14bp54 massive None gsc None zenodo None edi https://ror.org/0330j0z60 figshare https://ror.org/041mxqs23"},{"location":"DoiProviderEnum/#slots","title":"Slots","text":"Name Description doi_provider The authority, or organization, the DOI is associated with"},{"location":"DoiProviderEnum/#see-also","title":"See Also","text":"name: DoiProviderEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:DoiProviderEnum\n- nmdc:ProcessingInstitutionEnum\n- nmdc:ExecutionResourceEnum\nrank: 1000\npermissible_values:\n emsl:\n text: emsl\n meaning: https://ror.org/04rc0xn13\n title: EMSL\n aliases:\n - Environmental Molecular Sciences Laboratory\n - EMSL\n jgi:\n text: jgi\n meaning: https://ror.org/04xm1d337\n title: JGI\n aliases:\n - Joint Genome Institute\n - JGI\n kbase:\n text: kbase\n meaning: https://ror.org/01znn6x10\n title: KBase\n aliases:\n - KBase\n osti:\n text: osti\n meaning: https://ror.org/031478740\n title: OSTI\n aliases:\n - Office of Scientific and Technical Information\n - OSTI\n ess_dive:\n text: ess_dive\n meaning: https://ror.org/01t14bp54\n title: ESS-DIVE\n aliases:\n - ESS-DIVE\n - Environmental System Science Data Infrastructure for a Virtual Ecosystem\n massive:\n text: massive\n title: MassIVE\n aliases:\n - MassIVE\n - Mass Spectrometry Virtual Environment\n gsc:\n text: gsc\n title: GSC\n aliases:\n - GSC\n - Genomic Standards Consortium\n zenodo:\n text: zenodo\n title: Zenodo\n aliases:\n - Zenodo\n edi:\n text: edi\n meaning: https://ror.org/0330j0z60\n title: EDI\n aliases:\n - EDI\n - Environmental Data Initiative\n figshare:\n text: figshare\n meaning: https://ror.org/041mxqs23\n title: Figshare\n\nURI: DoorCompTypeEnum
"},{"location":"DoorCompTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metal covered None revolving None sliding None telescopic None"},{"location":"DoorCompTypeEnum/#slots","title":"Slots","text":"Name Description door_comp_type The composite type of the door"},{"location":"DoorCompTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCompTypeEnum/#schema-source","title":"Schema Source","text":"name: door_comp_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metal covered:\n text: metal covered\n revolving:\n text: revolving\n sliding:\n text: sliding\n telescopic:\n text: telescopic\n\nURI: DoorCondEnum
"},{"location":"DoorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"DoorCondEnum/#slots","title":"Slots","text":"Name Description door_cond The phsical condition of the door"},{"location":"DoorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCondEnum/#schema-source","title":"Schema Source","text":"name: door_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: DoorDirectEnum
"},{"location":"DoorDirectEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description inward None outward None sideways None"},{"location":"DoorDirectEnum/#slots","title":"Slots","text":"Name Description door_direct The direction the door opens"},{"location":"DoorDirectEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorDirectEnum/#schema-source","title":"Schema Source","text":"name: door_direct_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n inward:\n text: inward\n outward:\n text: outward\n sideways:\n text: sideways\n\nURI: DoorLocEnum
"},{"location":"DoorLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"DoorLocEnum/#slots","title":"Slots","text":"Name Description door_loc The relative location of the door in the room"},{"location":"DoorLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorLocEnum/#schema-source","title":"Schema Source","text":"name: door_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: DoorMatEnum
"},{"location":"DoorMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aluminum None cellular PVC None engineered plastic None fiberboard None fiberglass None metal None thermoplastic alloy None vinyl None wood None wood/plastic composite None"},{"location":"DoorMatEnum/#slots","title":"Slots","text":"Name Description door_mat The material the door is composed of"},{"location":"DoorMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMatEnum/#schema-source","title":"Schema Source","text":"name: door_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n aluminum:\n text: aluminum\n cellular PVC:\n text: cellular PVC\n engineered plastic:\n text: engineered plastic\n fiberboard:\n text: fiberboard\n fiberglass:\n text: fiberglass\n metal:\n text: metal\n thermoplastic alloy:\n text: thermoplastic alloy\n vinyl:\n text: vinyl\n wood:\n text: wood\n wood/plastic composite:\n text: wood/plastic composite\n\nURI: DoorMoveEnum
"},{"location":"DoorMoveEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None folding None revolving None rolling shutter None sliding None swinging None"},{"location":"DoorMoveEnum/#slots","title":"Slots","text":"Name Description door_move The type of movement of the door"},{"location":"DoorMoveEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMoveEnum/#schema-source","title":"Schema Source","text":"name: door_move_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n collapsible:\n text: collapsible\n folding:\n text: folding\n revolving:\n text: revolving\n rolling shutter:\n text: rolling shutter\n sliding:\n text: sliding\n swinging:\n text: swinging\n\nURI: DoorTypeEnum
"},{"location":"DoorTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description composite None metal None wooden None"},{"location":"DoorTypeEnum/#slots","title":"Slots","text":"Name Description door_type The type of door material"},{"location":"DoorTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeEnum/#schema-source","title":"Schema Source","text":"name: door_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n composite:\n text: composite\n metal:\n text: metal\n wooden:\n text: wooden\n\nURI: DoorTypeMetalEnum
"},{"location":"DoorTypeMetalEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None corrugated steel None hollow None rolling shutters None steel plate None"},{"location":"DoorTypeMetalEnum/#slots","title":"Slots","text":"Name Description door_type_metal The type of metal door"},{"location":"DoorTypeMetalEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeMetalEnum/#schema-source","title":"Schema Source","text":"name: door_type_metal_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n collapsible:\n text: collapsible\n corrugated steel:\n text: corrugated steel\n hollow:\n text: hollow\n rolling shutters:\n text: rolling shutters\n steel plate:\n text: steel plate\n\nURI: DoorTypeWoodEnum
"},{"location":"DoorTypeWoodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bettened and ledged None battened None ledged and braced None ledged and framed None ledged, braced and frame None framed and paneled None glashed or sash None flush None louvered None wire gauged None"},{"location":"DoorTypeWoodEnum/#slots","title":"Slots","text":"Name Description door_type_wood The type of wood door"},{"location":"DoorTypeWoodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeWoodEnum/#schema-source","title":"Schema Source","text":"name: door_type_wood_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bettened and ledged:\n text: bettened and ledged\n battened:\n text: battened\n ledged and braced:\n text: ledged and braced\n ledged and framed:\n text: ledged and framed\n ledged, braced and frame:\n text: ledged, braced and frame\n framed and paneled:\n text: framed and paneled\n glashed or sash:\n text: glashed or sash\n flush:\n text: flush\n louvered:\n text: louvered\n wire gauged:\n text: wire gauged\n\nA real number that conforms to the xsd:double specification
URI: xsd:double
base: float
uri: xsd:double
URI: DrainageClassEnum
"},{"location":"DrainageClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description very poorly None poorly None somewhat poorly None moderately well None well None excessively drained None"},{"location":"DrainageClassEnum/#slots","title":"Slots","text":"Name Description drainage_class Drainage classification from a standard system such as the USDA system"},{"location":"DrainageClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrainageClassEnum/#schema-source","title":"Schema Source","text":"name: drainage_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n very poorly:\n text: very poorly\n poorly:\n text: poorly\n somewhat poorly:\n text: somewhat poorly\n moderately well:\n text: moderately well\n well:\n text: well\n excessively drained:\n text: excessively drained\n\nURI: DrawingsEnum
"},{"location":"DrawingsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None building navigation map None diagram None sketch None"},{"location":"DrawingsEnum/#slots","title":"Slots","text":"Name Description drawings The buildings architectural drawings; if design is chosen, indicate phase-con..."},{"location":"DrawingsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrawingsEnum/#schema-source","title":"Schema Source","text":"name: drawings_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n operation:\n text: operation\n as built:\n text: as built\n construction:\n text: construction\n bid:\n text: bid\n design:\n text: design\n building navigation map:\n text: building navigation map\n diagram:\n text: diagram\n sketch:\n text: sketch\n\nURI: EluentIntroductionCategoryEnum
"},{"location":"EluentIntroductionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description liquid_chromatography None The processed sample is introduced into the mass spectrometer through a liqui... gas_chromatography None The processed sample is introduced into the mass spectrometer through a gas c... direct_infusion_syringe None The processed sample is introduced into the mass spectrometer through a direc... direct_infusion_autosampler None The processed sample is introduced into the mass spectrometer through a direc..."},{"location":"EluentIntroductionCategoryEnum/#slots","title":"Slots","text":"Name Description eluent_introduction_category A high-level categorization for how the processed sample is introduced into a..."},{"location":"EluentIntroductionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"EluentIntroductionCategoryEnum/#schema-source","title":"Schema Source","text":"name: EluentIntroductionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n liquid_chromatography:\n text: liquid_chromatography\n description: The processed sample is introduced into the mass spectrometer through\n a liquid chromatography process.\n aliases:\n - LC\n gas_chromatography:\n text: gas_chromatography\n description: The processed sample is introduced into the mass spectrometer through\n a gas chromatography process.\n aliases:\n - GC\n direct_infusion_syringe:\n text: direct_infusion_syringe\n description: The processed sample is introduced into the mass spectrometer through\n a direct infusion process using a syringe.\n direct_infusion_autosampler:\n text: direct_infusion_autosampler\n description: The processed sample is introduced into the mass spectrometer through\n a direct infusion process using an autosampler.\n\nURI: nmdc:EnvironmentalMaterialTerm
classDiagram\n class EnvironmentalMaterialTerm\n click EnvironmentalMaterialTerm href \"../EnvironmentalMaterialTerm\"\n OntologyClass <|-- EnvironmentalMaterialTerm\n click OntologyClass href \"../OntologyClass\"\n\n\n\n EnvironmentalMaterialTerm : alternative_identifiers\n\n EnvironmentalMaterialTerm : alternative_names\n\n EnvironmentalMaterialTerm : definition\n\n EnvironmentalMaterialTerm : description\n\n EnvironmentalMaterialTerm : id\n\n EnvironmentalMaterialTerm : name\n\n EnvironmentalMaterialTerm : relations\n\n EnvironmentalMaterialTerm --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n EnvironmentalMaterialTerm : type\n\n\n\nname: EnvironmentalMaterialTerm\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nclass_uri: nmdc:EnvironmentalMaterialTerm\n\nname: EnvironmentalMaterialTerm\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nattributes:\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: EnvironmentalMaterialTerm\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: EnvironmentalMaterialTerm\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: EnvironmentalMaterialTerm\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: EnvironmentalMaterialTerm\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: EnvironmentalMaterialTerm\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: EnvironmentalMaterialTerm\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: EnvironmentalMaterialTerm\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: EnvironmentalMaterialTerm\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:EnvironmentalMaterialTerm\n\nThis class contains information pertaining to evaluating if a Metagenome-Assembled Genome (MAG) is eukaryotic.
URI: nmdc:EukEval
classDiagram\n class EukEval\n click EukEval href \"../EukEval\"\n\n EukEval : completeness\n\n EukEval : contamination\n\n EukEval : ncbi_lineage\n\n EukEval : ncbi_lineage_tax_ids\n\n EukEval : type\n\n\n\nname: EukEval\ndescription: This class contains information pertaining to evaluating if a Metagenome-Assembled\n Genome (MAG) is eukaryotic.\ncomments:\n- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information\n for this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- type\n- completeness\n- contamination\n- ncbi_lineage_tax_ids\n- ncbi_lineage\nclass_uri: nmdc:EukEval\n\nname: EukEval\ndescription: This class contains information pertaining to evaluating if a Metagenome-Assembled\n Genome (MAG) is eukaryotic.\ncomments:\n- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information\n for this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: EukEval\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n completeness:\n name: completeness\n description: Estimate of the completeness of the metagenome-assembled genome,\n estimated by a tool like CheckM.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: completeness\n owner: EukEval\n domain_of:\n - EukEval\n - MagBin\n range: float\n minimum_value: 0\n contamination:\n name: contamination\n description: Estimate of the completeness of the metagenome-assembled genome,\n estimated by a tool like CheckM.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contamination\n owner: EukEval\n domain_of:\n - EukEval\n - MagBin\n range: float\n minimum_value: 0\n ncbi_lineage_tax_ids:\n name: ncbi_lineage_tax_ids\n description: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)\n comments:\n - Example 1-131567-2759-2611352-33682-191814-2603949\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_lineage_tax_ids\n owner: EukEval\n domain_of:\n - EukEval\n range: string\n pattern: ^\\d+(-\\d+)*$\n ncbi_lineage:\n name: ncbi_lineage\n description: Comma delimited ordered list of NCBI taxonomy names.\n comments:\n - Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_lineage\n owner: EukEval\n domain_of:\n - EukEval\n range: string\nclass_uri: nmdc:EukEval\n\nURI: ExecutionResourceEnum
"},{"location":"ExecutionResourceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description NERSC-Cori None NERSC Cori supercomputer NERSC-Perlmutter None NERSC Perlmutter supercomputer EMSL None Environmental Molecular Sciences Laboratory EMSL-RZR None Environmental Molecular Sciences Laboratory RZR cluster JGI None Joint Genome Institute LANL-B-div None LANL Bioscience Division"},{"location":"ExecutionResourceEnum/#slots","title":"Slots","text":"Name Description execution_resource The computing resource or facility where the workflow was executed"},{"location":"ExecutionResourceEnum/#see-also","title":"See Also","text":"name: ExecutionResourceEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:DoiProviderEnum\n- nmdc:ProcessingInstitutionEnum\n- nmdc:ExecutionResourceEnum\nrank: 1000\npermissible_values:\n NERSC-Cori:\n text: NERSC-Cori\n description: NERSC Cori supercomputer\n aliases:\n - Cori\n NERSC-Perlmutter:\n text: NERSC-Perlmutter\n description: NERSC Perlmutter supercomputer\n aliases:\n - Perlmutter\n - Saul\n EMSL:\n text: EMSL\n description: Environmental Molecular Sciences Laboratory\n EMSL-RZR:\n text: EMSL-RZR\n description: Environmental Molecular Sciences Laboratory RZR cluster\n aliases:\n - RZR\n JGI:\n text: JGI\n description: Joint Genome Institute\n LANL-B-div:\n text: LANL-B-div\n description: LANL Bioscience Division\n aliases:\n - B-div\n\nURI: ExtWallOrientEnum
"},{"location":"ExtWallOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWallOrientEnum/#slots","title":"Slots","text":"Name Description ext_wall_orient The orientation of the exterior wall"},{"location":"ExtWallOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWallOrientEnum/#schema-source","title":"Schema Source","text":"name: ext_wall_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n northeast:\n text: northeast\n southeast:\n text: southeast\n southwest:\n text: southwest\n northwest:\n text: northwest\n\nURI: ExtWindowOrientEnum
"},{"location":"ExtWindowOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWindowOrientEnum/#slots","title":"Slots","text":"Name Description ext_window_orient The compass direction the exterior window of the room is facing"},{"location":"ExtWindowOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWindowOrientEnum/#schema-source","title":"Schema Source","text":"name: ext_window_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n northeast:\n text: northeast\n southeast:\n text: southeast\n southwest:\n text: southwest\n northwest:\n text: northwest\n\nA CURIE representing an external identifier
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
typeof: uriorcurie
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
A material separation in which a desired component of an input material is separated from the remainder.
URI: nmdc:Extraction
classDiagram\n class Extraction\n click Extraction href \"../Extraction\"\n MaterialProcessing <|-- Extraction\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n Extraction : alternative_identifiers\n\n Extraction : description\n\n Extraction : end_date\n\n Extraction : extraction_targets\n\n Extraction --> \"*\" ExtractionTargetEnum : extraction_targets\n click ExtractionTargetEnum href \"../ExtractionTargetEnum\"\n\n Extraction : has_failure_categorization\n\n Extraction --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n Extraction : has_input\n\n Extraction --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n Extraction : has_output\n\n Extraction --> \"1..*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n Extraction : id\n\n Extraction : input_mass\n\n Extraction --> \"0..1\" QuantityValue : input_mass\n click QuantityValue href \"../QuantityValue\"\n\n Extraction : instrument_used\n\n Extraction --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n Extraction : name\n\n Extraction : processing_institution\n\n Extraction --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n Extraction : protocol_link\n\n Extraction --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n Extraction : qc_comment\n\n Extraction : qc_status\n\n Extraction --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n Extraction : start_date\n\n Extraction : substances_used\n\n Extraction --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n Extraction : type\n\n Extraction : volume\n\n Extraction --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: Extraction\ndescription: A material separation in which a desired component of an input material\n is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: MaterialProcessing\nslots:\n- substances_used\n- extraction_targets\n- input_mass\n- volume\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The volume of the solvent/solute being used, not the input.\nclass_uri: nmdc:Extraction\n\nname: Extraction\ndescription: A material separation in which a desired component of an input material\n is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: MaterialProcessing\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The volume of the solvent/solute being used, not the input.\nattributes:\n substances_used:\n name: substances_used\n description: The substances that are combined to enable a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: Extraction\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n extraction_targets:\n name: extraction_targets\n description: Provides the target biomolecule that has been separated from a sample\n during an extraction process.\n notes:\n - todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)\n from_schema: https://w3id.org/nmdc/nmdc\n narrow_mappings:\n - NCIT:C177560\n - MIXS:0000037\n rank: 1000\n alias: extraction_targets\n owner: Extraction\n domain_of:\n - Extraction\n range: ExtractionTargetEnum\n multivalued: true\n input_mass:\n name: input_mass\n description: Total mass of sample used in activity.\n title: sample mass used\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample mass\n - sample weight\n exact_mappings:\n - MS:1000004\n narrow_mappings:\n - MIXS:0000111\n rank: 1000\n alias: input_mass\n owner: Extraction\n domain_of:\n - Extraction\n range: QuantityValue\n volume:\n name: volume\n description: The volume of the solvent/solute being used, not the input.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: Extraction\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: Extraction\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Extraction\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Extraction\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Extraction\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Extraction\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Extraction\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Extraction\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Extraction\n\nURI: ExtractionTargetEnum
"},{"location":"ExtractionTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None metabolite None protein None lipid None"},{"location":"ExtractionTargetEnum/#slots","title":"Slots","text":"Name Description extraction_targets Provides the target biomolecule that has been separated from a sample during ..."},{"location":"ExtractionTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtractionTargetEnum/#schema-source","title":"Schema Source","text":"name: ExtractionTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DNA:\n text: DNA\n RNA:\n text: RNA\n metabolite:\n text: metabolite\n protein:\n text: protein\n lipid:\n text: lipid\n\nURI: nmdc:FailureCategorization
classDiagram\n class FailureCategorization\n click FailureCategorization href \"../FailureCategorization\"\n\n FailureCategorization : qc_failure_what\n\n FailureCategorization --> \"0..1\" FailureWhatEnum : qc_failure_what\n click FailureWhatEnum href \"../FailureWhatEnum\"\n\n FailureCategorization : qc_failure_where\n\n FailureCategorization --> \"0..1\" FailureWhereEnum : qc_failure_where\n click FailureWhereEnum href \"../FailureWhereEnum\"\n\n FailureCategorization : type\n\n\n\nname: FailureCategorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- qc_failure_what\n- qc_failure_where\n- type\nclass_uri: nmdc:FailureCategorization\n\nname: FailureCategorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n qc_failure_what:\n name: qc_failure_what\n description: Provides a summary about what caused a lab or workflow process to\n fail\n comments:\n - For example, low read count from a sequencer, malformed fastq files, etc.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_failure_what\n owner: FailureCategorization\n domain_of:\n - FailureCategorization\n range: FailureWhatEnum\n qc_failure_where:\n name: qc_failure_where\n description: Describes the nmdc schema class that corresonds to where the failure\n occurred. Most commonly this would be the same as Class that generated the results.\n comments:\n - If the assembly size was too small to proceed to annotation failure_where would\n be MetagenomeAssembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_failure_where\n owner: FailureCategorization\n domain_of:\n - FailureCategorization\n range: FailureWhereEnum\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FailureCategorization\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FailureCategorization\n\nThe permitted values for describing where a failure occurred during processing in the lab during analysis workflows.
URI: FailureWhatEnum
"},{"location":"FailureWhatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low_read_count None Number of output reads is not sufficient to continue to the next analysis ste... malformed_data None Workflow failure reading input or writing the output file(s) assembly_size_too_small None The size of the metagenome or metatranscriptome assembly is too small to proc... no_valid_data_generated None A process ran but did not produce any output other None A lab process or analysis workflow has failed in a way that has not been capt..."},{"location":"FailureWhatEnum/#slots","title":"Slots","text":"Name Description qc_failure_what Provides a summary about what caused a lab or workflow process to fail"},{"location":"FailureWhatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FailureWhatEnum/#schema-source","title":"Schema Source","text":"name: FailureWhatEnum\ndescription: The permitted values for describing where a failure occurred during processing\n in the lab during analysis workflows.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n low_read_count:\n text: low_read_count\n description: Number of output reads is not sufficient to continue to the next\n analysis step.\n malformed_data:\n text: malformed_data\n description: Workflow failure reading input or writing the output file(s).\n assembly_size_too_small:\n text: assembly_size_too_small\n description: The size of the metagenome or metatranscriptome assembly is too small\n to proceed to the next analysis workflow.\n no_valid_data_generated:\n text: no_valid_data_generated\n description: A process ran but did not produce any output. Ie binning ran but\n did not produce any medium or high quality bins.\n other:\n text: other\n description: A lab process or analysis workflow has failed in a way that has not\n been captured by the available values yet. Please use slot 'qc_comment' to specify\n details.\n\nThe permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.
URI: FailureWhereEnum
"},{"location":"FailureWhereEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description NucleotideSequencing None A failure has occurred during nucleotide sequencing, a data generation proces... MassSpectrometry None A failure has occurred during mass spectrometry, a data generation process Pooling None A failure has occurred in pooling, a lab process Extraction None A failure has occurred in extraction, a lab process LibraryPreparation None A failure has occurred in library preparation, a lab process MetagenomeAssembly None A failure has occurred in metagenome assembly, a workflow process MetatranscriptomeExpressionAnalysis None A failure has occurred in metatranscriptome expression analysis, a workflow p... MagsAnalysis None A failure has occurred in binning, a workflow process to generate metagenome-... ReadQcAnalysis None A failure has occurred in read qc, a workflow process ReadBasedTaxonomyAnalysis None A failure has occurred in reads based taxonomy, a workflow process MetagenomeAnnotation None A failure has occurred in annotation, a workflow process MetatranscriptomeAssembly None A failure has occurred in assembly, a workflow process MetatranscriptomeAnnotation None A failure has occurred in annotation, a workflow process MetabolomicsAnalysis None A failure has occurred in analyzing metabolomics data MetaproteomicsAnalysis None A failure has occurred in analyzing metaproteomics data NomAnalysis None A failure has occurred in analyzing NOM data"},{"location":"FailureWhereEnum/#slots","title":"Slots","text":"Name Description qc_failure_where Describes the nmdc schema class that corresonds to where the failure occurred"},{"location":"FailureWhereEnum/#comments","title":"Comments","text":"name: FailureWhereEnum\ndescription: The permitted values for describing where in the process, either a lab\n or analysis workflow step, the failure occurred.\ncomments:\n- At Chris' recommendation permissible values for this enumeration are the same as\n Class names.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n NucleotideSequencing:\n text: NucleotideSequencing\n description: A failure has occurred during nucleotide sequencing, a data generation\n process.\n MassSpectrometry:\n text: MassSpectrometry\n description: A failure has occurred during mass spectrometry, a data generation\n process.\n Pooling:\n text: Pooling\n description: A failure has occurred in pooling, a lab process.\n Extraction:\n text: Extraction\n description: A failure has occurred in extraction, a lab process.\n LibraryPreparation:\n text: LibraryPreparation\n description: A failure has occurred in library preparation, a lab process.\n MetagenomeAssembly:\n text: MetagenomeAssembly\n description: A failure has occurred in metagenome assembly, a workflow process.\n MetatranscriptomeExpressionAnalysis:\n text: MetatranscriptomeExpressionAnalysis\n description: A failure has occurred in metatranscriptome expression analysis,\n a workflow process.\n MagsAnalysis:\n text: MagsAnalysis\n description: A failure has occurred in binning, a workflow process to generate\n metagenome-assembled genomes (MAGS).\n ReadQcAnalysis:\n text: ReadQcAnalysis\n description: A failure has occurred in read qc, a workflow process.\n ReadBasedTaxonomyAnalysis:\n text: ReadBasedTaxonomyAnalysis\n description: A failure has occurred in reads based taxonomy, a workflow process.\n MetagenomeAnnotation:\n text: MetagenomeAnnotation\n description: A failure has occurred in annotation, a workflow process.\n MetatranscriptomeAssembly:\n text: MetatranscriptomeAssembly\n description: A failure has occurred in assembly, a workflow process.\n MetatranscriptomeAnnotation:\n text: MetatranscriptomeAnnotation\n description: A failure has occurred in annotation, a workflow process.\n MetabolomicsAnalysis:\n text: MetabolomicsAnalysis\n description: A failure has occurred in analyzing metabolomics data.\n MetaproteomicsAnalysis:\n text: MetaproteomicsAnalysis\n description: A failure has occurred in analyzing metaproteomics data.\n NomAnalysis:\n text: NomAnalysis\n description: A failure has occurred in analyzing NOM data.\n\nURI: FaoClassEnum
"},{"location":"FaoClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Acrisols None Andosols None Arenosols None Cambisols None Chernozems None Ferralsols None Fluvisols None Gleysols None Greyzems None Gypsisols None Histosols None Kastanozems None Lithosols None Luvisols None Nitosols None Phaeozems None Planosols None Podzols None Podzoluvisols None Rankers None Regosols None Rendzinas None Solonchaks None Solonetz None Vertisols None Yermosols None"},{"location":"FaoClassEnum/#slots","title":"Slots","text":"Name Description fao_class Soil classification from the FAO World Reference Database for Soil Resources"},{"location":"FaoClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FaoClassEnum/#schema-source","title":"Schema Source","text":"name: fao_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Acrisols:\n text: Acrisols\n Andosols:\n text: Andosols\n Arenosols:\n text: Arenosols\n Cambisols:\n text: Cambisols\n Chernozems:\n text: Chernozems\n Ferralsols:\n text: Ferralsols\n Fluvisols:\n text: Fluvisols\n Gleysols:\n text: Gleysols\n Greyzems:\n text: Greyzems\n Gypsisols:\n text: Gypsisols\n Histosols:\n text: Histosols\n Kastanozems:\n text: Kastanozems\n Lithosols:\n text: Lithosols\n Luvisols:\n text: Luvisols\n Nitosols:\n text: Nitosols\n Phaeozems:\n text: Phaeozems\n Planosols:\n text: Planosols\n Podzols:\n text: Podzols\n Podzoluvisols:\n text: Podzoluvisols\n Rankers:\n text: Rankers\n Regosols:\n text: Regosols\n Rendzinas:\n text: Rendzinas\n Solonchaks:\n text: Solonchaks\n Solonetz:\n text: Solonetz\n Vertisols:\n text: Vertisols\n Yermosols:\n text: Yermosols\n\nA site, outside of a laboratory, from which biosamples may be collected.
URI: nmdc:FieldResearchSite
classDiagram\n class FieldResearchSite\n click FieldResearchSite href \"../FieldResearchSite\"\n Site <|-- FieldResearchSite\n click Site href \"../Site\"\n\n\n\n FieldResearchSite : alternative_identifiers\n\n FieldResearchSite : cur_vegetation\n\n FieldResearchSite --> \"0..1\" TextValue : cur_vegetation\n click TextValue href \"../TextValue\"\n\n FieldResearchSite : description\n\n FieldResearchSite : elev\n\n FieldResearchSite : geo_loc_name\n\n FieldResearchSite --> \"0..1\" TextValue : geo_loc_name\n click TextValue href \"../TextValue\"\n\n FieldResearchSite : habitat\n\n FieldResearchSite : id\n\n FieldResearchSite : lat_lon\n\n FieldResearchSite --> \"0..1\" GeolocationValue : lat_lon\n click GeolocationValue href \"../GeolocationValue\"\n\n FieldResearchSite : local_class\n\n FieldResearchSite --> \"0..1\" TextValue : local_class\n click TextValue href \"../TextValue\"\n\n FieldResearchSite : name\n\n FieldResearchSite : part_of\n\n FieldResearchSite --> \"*\" FieldResearchSite : part_of\n click FieldResearchSite href \"../FieldResearchSite\"\n\n FieldResearchSite : soil_type\n\n FieldResearchSite --> \"0..1\" TextValue : soil_type\n click TextValue href \"../TextValue\"\n\n FieldResearchSite : type\n\n\n\nname: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n same plant were obtained at the same site. In this case, the site would correspond\n to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslots:\n- cur_vegetation\n- elev\n- geo_loc_name\n- habitat\n- lat_lon\n- local_class\n- part_of\n- soil_type\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n part_of:\n name: part_of\n range: FieldResearchSite\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:FieldResearchSite\n\nname: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n same plant were obtained at the same site. In this case, the site would correspond\n to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n part_of:\n name: part_of\n range: FieldResearchSite\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n cur_vegetation:\n name: cur_vegetation\n annotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n title: current vegetation\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current vegetation\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000312\n alias: cur_vegetation\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n elev:\n name: elev\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the\n surface, such as an aircraft in flight or a spacecraft in orbit.\n title: elevation\n examples:\n - value: 100 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevation\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000093\n alias: elev\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n multivalued: false\n geo_loc_name:\n name: geo_loc_name\n annotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n name'\n description: The geographical origin of the sample as defined by the country or\n sea name followed by specific region name. Country or sea names should be chosen\n from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n (http://purl.bioontology.org/ontology/GAZ)\n title: geographic location (country and/or sea,region)\n examples:\n - value: 'USA: Maryland, Bethesda'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (country and/or sea,region)\n rank: 1000\n is_a: environment field\n string_serialization: '{term}: {term}, {text}'\n slot_uri: MIXS:0000010\n alias: geo_loc_name\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n habitat:\n name: habitat\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: habitat\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: string\n lat_lon:\n name: lat_lon\n annotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\n description: The geographical origin of the sample as defined by latitude and\n longitude. The values should be reported in decimal degrees and in WGS84 system\n title: geographic location (latitude and longitude)\n examples:\n - value: 50.586825 6.408977\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (latitude and longitude)\n rank: 1000\n is_a: environment field\n string_serialization: '{float} {float}'\n slot_uri: MIXS:0000009\n alias: lat_lon\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: GeolocationValue\n multivalued: false\n local_class:\n name: local_class\n annotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification based on local soil classification system\n title: soil_taxonomic/local classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000330\n alias: local_class\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n slot_uri: dcterms:isPartOf\n alias: part_of\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Study\n range: FieldResearchSite\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n soil_type:\n name: soil_type\n annotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of the soil type or classification. This field accepts\n terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms\n can be separated by pipes.\n title: soil type\n examples:\n - value: plinthosol [ENVO:00002250]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000332\n alias: soil_type\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: FieldResearchSite\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FieldResearchSite\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FieldResearchSite\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: FieldResearchSite\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FieldResearchSite\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FieldResearchSite\n\nURI: FileTypeEnum
"},{"location":"FileTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Virus Summary None Tab separated file listing the viruses found by geNomad Plasmid Summary None Tab separated file listing the plasmids found be geNomad GeNomad Aggregated Classification None Tab separated file which combines the results from neural network-based class... Reference Calibration File None A file that contains data used to calibrate a natural organic matter or metab... Metagenome Raw Reads None Interleaved paired-end raw sequencing data Metagenome Raw Read 1 None Read 1 raw sequencing data, aka forward reads Metagenome Raw Read 2 None Read 2 raw sequencing data, aka reverse reads FT ICR-MS Analysis Results None FT ICR-MS-based molecular formula assignment results table GC-MS Metabolomics Results None GC-MS-based metabolite assignment results table Metaproteomics Workflow Statistics None Aggregate workflow statistics file Protein Report None Filtered protein report file Peptide Report None Filtered peptide report file Unfiltered Metaproteomics Results None MSGFjobs and MASIC output file Read Count and RPKM None Annotation read count and RPKM per feature JSON QC non-rRNA R2 None QC removed rRNA reads (R2) fastq QC non-rRNA R1 None QC removed rRNA reads (R1) fastq Metagenome Bins None Metagenome bin contigs fasta Metagenome HQMQ Bins Compression File None Compressed file containing high qulaity and medium quality metagenome bins an... Metagenome LQ Bins Compression File None Compressed file containing low quality metagenome bins and associated files Metagenome Bins Info File None File containing version information on the binning workflow CheckM Statistics None CheckM statistics report Metagenome Bins Heatmap None The Heatmap presents the pdf file containing the KO analysis results for meta... Metagenome Bins Barplot None The Bar chart presents the pdf file containing the KO analysis results for me... Metagenome Bins Krona Plot None The Krona plot presents the HTML file containing the KO analysis results for ... Read Based Analysis Info File None File containing reads based analysis information GTDBTK Bacterial Summary None GTDBTK bacterial summary GTDBTK Archaeal Summary None GTDBTK archaeal summary GOTTCHA2 Krona Plot None GOTTCHA2 krona plot HTML file GOTTCHA2 Classification Report None GOTTCHA2 classification report file GOTTCHA2 Report Full None GOTTCHA2 report file Kraken2 Krona Plot None Kraken2 krona plot HTML file Centrifuge Krona Plot None Centrifuge krona plot HTML file Centrifuge output report file None Centrifuge output report file Kraken2 Classification Report None Kraken2 output report file Kraken2 Taxonomic Classification None Kraken2 output read classification file Centrifuge Classification Report None Centrifuge output report file Centrifuge Taxonomic Classification None Centrifuge output read classification file Structural Annotation GFF None GFF3 format file with structural annotations Structural Annotation Stats Json None Structural annotations stats json Functional Annotation GFF None GFF3 format file with functional annotations Annotation Info File None File containing annotation info Annotation Amino Acid FASTA None FASTA amino acid file for annotated proteins Annotation Enzyme Commission None Tab delimited file for EC annotation Annotation KEGG Orthology None Tab delimited file for KO annotation Assembly Info File None File containing assembly info Assembly Coverage BAM None Sorted bam file of reads mapping back to the final assembly Assembly AGP None An AGP format file that describes the assembly Assembly Scaffolds None Final assembly scaffolds fasta Assembly Contigs None Final assembly contigs fasta Assembly Coverage Stats None Assembled contigs coverage information Contig Mapping File None Contig mappings between contigs and scaffolds Error Corrected Reads None Error corrected reads fastq Filtered Sequencing Reads None Reads QC result fastq (clean data) Read Filtering Info File None File containing read filtering information QC Statistics Extended None Extended report including methods and results for read filtering QC Statistics None Reads QC summary statistics TIGRFam Annotation GFF None GFF3 format file with TIGRfam CRT Annotation GFF None GFF3 format file with CRT Genemark Annotation GFF None GFF3 format file with Genemark Prodigal Annotation GFF None GFF3 format file with Prodigal TRNA Annotation GFF None GFF3 format file with TRNA Misc Annotation GFF None GFF3 format file with Misc RFAM Annotation GFF None GFF3 format file with RFAM TMRNA Annotation GFF None GFF3 format file with TMRNA Crispr Terms None Crispr Terms Product Names None Product names file Gene Phylogeny tsv None Gene Phylogeny tsv Scaffold Lineage tsv None phylogeny at the scaffold level Clusters of Orthologous Groups (COG) Annotation GFF None GFF3 format file with COGs KO_EC Annotation GFF None GFF3 format file with KO_EC CATH FunFams (Functional Families) Annotation GFF None GFF3 format file with CATH FunFams SUPERFam Annotation GFF None GFF3 format file with SUPERFam SMART Annotation GFF None GFF3 format file with SMART Pfam Annotation GFF None GFF3 format file with Pfam Annotation Statistics None Annotation statistics report Direct Infusion FT ICR-MS Raw Data None Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance mass spect... LC-DDA-MS/MS Raw Data None Liquid chromatographically separated MS1 and Data-Dependent MS2 binary instru... Configuration toml None A configuration toml file used by various programs to store settings that are... LC-MS Lipidomics Results None LC-MS-based lipidomics analysis results table LC-MS Lipidomics Processed Data None Processed data for the LC-MS-based lipidomics analysis in hdf5 format Contaminants Amino Acid FASTA None FASTA amino acid file for contaminant proteins commonly observed in proteomic... Analysis Tool Parameter File None A configuration file used by a single computational software tool that stores... Workflow Operation Summary None A human readable record of analysis steps applied during an instance of a wor... Metatranscriptome Expression None Metatranscriptome expression values and read counts for gene features predict... Metatranscriptome Expression Intergenic None Metatranscriptome expression values and read counts for intergenic regions Metatranscriptome Expression Info File None File containing version information on the expression workflow rRNA Filtered Sequencing Reads None File containing ribosomal reads from the read qc filtering step BAI File None An index file found in the same directory as the binary alignment map (BAM) f..."},{"location":"FileTypeEnum/#slots","title":"Slots","text":"Name Description data_object_type The type of file represented by the data object"},{"location":"FileTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FileTypeEnum/#schema-source","title":"Schema Source","text":"name: FileTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Virus Summary:\n text: Virus Summary\n description: Tab separated file listing the viruses found by geNomad.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^_virus_summary\\.tsv?$\n see_also:\n - https://portal.nersc.gov/genomad/\n Plasmid Summary:\n text: Plasmid Summary\n description: Tab separated file listing the plasmids found be geNomad.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^_plasmid_summary\\.tsv?$\n see_also:\n - https://portal.nersc.gov/genomad/\n GeNomad Aggregated Classification:\n text: GeNomad Aggregated Classification\n description: Tab separated file which combines the results from neural network-based\n classification and marker-based classification for virus and plasmid detection\n with geNomad.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^_aggregated_classification\\.tsv?$\n see_also:\n - https://portal.nersc.gov/genomad/\n Reference Calibration File:\n text: Reference Calibration File\n description: A file that contains data used to calibrate a natural organic matter\n or metabalomics analysis.\n Metagenome Raw Reads:\n text: Metagenome Raw Reads\n description: Interleaved paired-end raw sequencing data\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^\\.fastq(\\.gz)?$\n Metagenome Raw Read 1:\n text: Metagenome Raw Read 1\n description: Read 1 raw sequencing data, aka forward reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^.+_R1\\.fastq(\\.gz)?$\n examples:\n - value: BMI_H25VYBGXH_19S_31WellG1_R1.fastq.gz\n Metagenome Raw Read 2:\n text: Metagenome Raw Read 2\n description: Read 2 raw sequencing data, aka reverse reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^.+_R2\\.fastq(\\.gz)?$\n examples:\n - value: BMI_H25VYBGXH_19S_31WellG1_R2.fastq.gz\n FT ICR-MS Analysis Results:\n text: FT ICR-MS Analysis Results\n description: FT ICR-MS-based molecular formula assignment results table\n GC-MS Metabolomics Results:\n text: GC-MS Metabolomics Results\n description: GC-MS-based metabolite assignment results table\n Metaproteomics Workflow Statistics:\n text: Metaproteomics Workflow Statistics\n description: Aggregate workflow statistics file\n Protein Report:\n text: Protein Report\n description: Filtered protein report file\n Peptide Report:\n text: Peptide Report\n description: Filtered peptide report file\n Unfiltered Metaproteomics Results:\n text: Unfiltered Metaproteomics Results\n description: MSGFjobs and MASIC output file\n Read Count and RPKM:\n text: Read Count and RPKM\n description: Annotation read count and RPKM per feature JSON\n QC non-rRNA R2:\n text: QC non-rRNA R2\n description: QC removed rRNA reads (R2) fastq\n QC non-rRNA R1:\n text: QC non-rRNA R1\n description: QC removed rRNA reads (R1) fastq\n Metagenome Bins:\n text: Metagenome Bins\n description: Metagenome bin contigs fasta\n Metagenome HQMQ Bins Compression File:\n text: Metagenome HQMQ Bins Compression File\n description: Compressed file containing high qulaity and medium quality metagenome\n bins and associated files\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_hqmq_bin.zip'\n Metagenome LQ Bins Compression File:\n text: Metagenome LQ Bins Compression File\n description: Compressed file containing low quality metagenome bins and associated\n files\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_lq_bin.zip'\n Metagenome Bins Info File:\n text: Metagenome Bins Info File\n description: File containing version information on the binning workflow\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_bin.info'\n CheckM Statistics:\n text: CheckM Statistics\n description: CheckM statistics report\n Metagenome Bins Heatmap:\n text: Metagenome Bins Heatmap\n description: The Heatmap presents the pdf file containing the KO analysis results\n for metagenome bins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_heatmap.pdf'\n Metagenome Bins Barplot:\n text: Metagenome Bins Barplot\n description: The Bar chart presents the pdf file containing the KO analysis results\n for metagenome bins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_barplot.pdf'\n Metagenome Bins Krona Plot:\n text: Metagenome Bins Krona Plot\n description: The Krona plot presents the HTML file containing the KO analysis\n results for metagenome bins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_kronaplot.html'\n Read Based Analysis Info File:\n text: Read Based Analysis Info File\n description: File containing reads based analysis information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: profiler.info\n GTDBTK Bacterial Summary:\n text: GTDBTK Bacterial Summary\n description: GTDBTK bacterial summary\n GTDBTK Archaeal Summary:\n text: GTDBTK Archaeal Summary\n description: GTDBTK archaeal summary\n GOTTCHA2 Krona Plot:\n text: GOTTCHA2 Krona Plot\n description: GOTTCHA2 krona plot HTML file\n GOTTCHA2 Classification Report:\n text: GOTTCHA2 Classification Report\n description: GOTTCHA2 classification report file\n GOTTCHA2 Report Full:\n text: GOTTCHA2 Report Full\n description: GOTTCHA2 report file\n Kraken2 Krona Plot:\n text: Kraken2 Krona Plot\n description: Kraken2 krona plot HTML file\n Centrifuge Krona Plot:\n text: Centrifuge Krona Plot\n description: Centrifuge krona plot HTML file\n Centrifuge output report file:\n text: Centrifuge output report file\n description: Centrifuge output report file\n Kraken2 Classification Report:\n text: Kraken2 Classification Report\n description: Kraken2 output report file\n Kraken2 Taxonomic Classification:\n text: Kraken2 Taxonomic Classification\n description: Kraken2 output read classification file\n Centrifuge Classification Report:\n text: Centrifuge Classification Report\n description: Centrifuge output report file\n Centrifuge Taxonomic Classification:\n text: Centrifuge Taxonomic Classification\n description: Centrifuge output read classification file\n Structural Annotation GFF:\n text: Structural Annotation GFF\n description: GFF3 format file with structural annotations\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_structural_annotation.gff'\n Structural Annotation Stats Json:\n text: Structural Annotation Stats Json\n description: Structural annotations stats json\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_structural_annotation_stats.json'\n Functional Annotation GFF:\n text: Functional Annotation GFF\n description: GFF3 format file with functional annotations\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_functional_annotation.gff'\n Annotation Info File:\n text: Annotation Info File\n description: File containing annotation info\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_imgap.info'\n Annotation Amino Acid FASTA:\n text: Annotation Amino Acid FASTA\n description: FASTA amino acid file for annotated proteins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_proteins.faa'\n Annotation Enzyme Commission:\n text: Annotation Enzyme Commission\n description: Tab delimited file for EC annotation\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ec.tsv'\n Annotation KEGG Orthology:\n text: Annotation KEGG Orthology\n description: Tab delimited file for KO annotation\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ko.tsv'\n Assembly Info File:\n text: Assembly Info File\n description: File containing assembly info\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: README.txt\n Assembly Coverage BAM:\n text: Assembly Coverage BAM\n description: Sorted bam file of reads mapping back to the final assembly\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pairedMapped.sam.gz'\n Assembly AGP:\n text: Assembly AGP\n description: An AGP format file that describes the assembly\n Assembly Scaffolds:\n text: Assembly Scaffolds\n description: Final assembly scaffolds fasta\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_assembly.contigs.fasta'\n Assembly Contigs:\n text: Assembly Contigs\n description: Final assembly contigs fasta\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: assembly.contigs.fasta\n Assembly Coverage Stats:\n text: Assembly Coverage Stats\n description: Assembled contigs coverage information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pairedMapped_sorted.bam.cov'\n Contig Mapping File:\n text: Contig Mapping File\n description: Contig mappings between contigs and scaffolds\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_contig_names_mapping.tsv'\n Error Corrected Reads:\n text: Error Corrected Reads\n description: Error corrected reads fastq\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: input.corr.fastq.gz\n Filtered Sequencing Reads:\n text: Filtered Sequencing Reads\n description: Reads QC result fastq (clean data)\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '/.+?(?=filter)/filter-METAGENOME.fastq.gz '\n Read Filtering Info File:\n text: Read Filtering Info File\n description: File containing read filtering information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[rqc_wf_activity_id]_readsQC.info'\n QC Statistics Extended:\n text: QC Statistics Extended\n description: Extended report including methods and results for read filtering\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: /.+?(?=filter)/filtered-report.txt\n QC Statistics:\n text: QC Statistics\n description: Reads QC summary statistics\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[rqc_wf_activity_id]_filterStats2.txt'\n TIGRFam Annotation GFF:\n text: TIGRFam Annotation GFF\n description: GFF3 format file with TIGRfam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_tigrfam.gff'\n CRT Annotation GFF:\n text: CRT Annotation GFF\n description: GFF3 format file with CRT\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_crt.gff'\n Genemark Annotation GFF:\n text: Genemark Annotation GFF\n description: GFF3 format file with Genemark\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_genemark.gff'\n Prodigal Annotation GFF:\n text: Prodigal Annotation GFF\n description: GFF3 format file with Prodigal\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_prodigal.gff'\n TRNA Annotation GFF:\n text: TRNA Annotation GFF\n description: GFF3 format file with TRNA\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_trna.gff'\n Misc Annotation GFF:\n text: Misc Annotation GFF\n description: GFF3 format file with Misc\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff'\n RFAM Annotation GFF:\n text: RFAM Annotation GFF\n description: GFF3 format file with RFAM\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam.gff'\n TMRNA Annotation GFF:\n text: TMRNA Annotation GFF\n description: GFF3 format file with TMRNA\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam_ncrna_tmrna.gff'\n Crispr Terms:\n text: Crispr Terms\n description: Crispr Terms\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_crt.crisprs'\n Product Names:\n text: Product Names\n description: Product names file\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_product_names.tsv'\n Gene Phylogeny tsv:\n text: Gene Phylogeny tsv\n description: Gene Phylogeny tsv\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_gene_phylogeny.tsv'\n Scaffold Lineage tsv:\n text: Scaffold Lineage tsv\n description: phylogeny at the scaffold level\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_scaffold_lineage.tsv'\n Clusters of Orthologous Groups (COG) Annotation GFF:\n text: Clusters of Orthologous Groups (COG) Annotation GFF\n description: GFF3 format file with COGs\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_cog.gff'\n KO_EC Annotation GFF:\n text: KO_EC Annotation GFF\n description: GFF3 format file with KO_EC\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ko_ec.gff'\n CATH FunFams (Functional Families) Annotation GFF:\n text: CATH FunFams (Functional Families) Annotation GFF\n description: GFF3 format file with CATH FunFams\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_cath_funfam.gff'\n SUPERFam Annotation GFF:\n text: SUPERFam Annotation GFF\n description: GFF3 format file with SUPERFam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_supfam.gff'\n SMART Annotation GFF:\n text: SMART Annotation GFF\n description: GFF3 format file with SMART\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_smart.gff'\n Pfam Annotation GFF:\n text: Pfam Annotation GFF\n description: GFF3 format file with Pfam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pfam.gff'\n Annotation Statistics:\n text: Annotation Statistics\n description: Annotation statistics report\n Direct Infusion FT ICR-MS Raw Data:\n text: Direct Infusion FT ICR-MS Raw Data\n description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance\n mass spectrometry raw data acquired in broadband full scan mode\n LC-DDA-MS/MS Raw Data:\n text: LC-DDA-MS/MS Raw Data\n description: Liquid chromatographically separated MS1 and Data-Dependent MS2 binary\n instrument file\n Configuration toml:\n text: Configuration toml\n description: A configuration toml file used by various programs to store settings\n that are specific to their respective software.\n broad_mappings:\n - edam.format:4005\n LC-MS Lipidomics Results:\n text: LC-MS Lipidomics Results\n description: LC-MS-based lipidomics analysis results table\n LC-MS Lipidomics Processed Data:\n text: LC-MS Lipidomics Processed Data\n description: Processed data for the LC-MS-based lipidomics analysis in hdf5 format\n Contaminants Amino Acid FASTA:\n text: Contaminants Amino Acid FASTA\n description: FASTA amino acid file for contaminant proteins commonly observed\n in proteomics data.\n Analysis Tool Parameter File:\n text: Analysis Tool Parameter File\n description: A configuration file used by a single computational software tool\n that stores settings that are specific to that tool.\n Workflow Operation Summary:\n text: Workflow Operation Summary\n description: A human readable record of analysis steps applied during an instance\n of a workflow operation.\n Metatranscriptome Expression:\n text: Metatranscriptome Expression\n description: Metatranscriptome expression values and read counts for gene features\n predicted on contigs\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*.rnaseq_gea.txt'\n Metatranscriptome Expression Intergenic:\n text: Metatranscriptome Expression Intergenic\n description: Metatranscriptome expression values and read counts for intergenic\n regions.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*.rnaseq_gea.intergenic.txt'\n Metatranscriptome Expression Info File:\n text: Metatranscriptome Expression Info File\n description: File containing version information on the expression workflow\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*_readcount.info'\n rRNA Filtered Sequencing Reads:\n text: rRNA Filtered Sequencing Reads\n description: File containing ribosomal reads from the read qc filtering step.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*.rRNA.fastq.gz'\n BAI File:\n text: BAI File\n description: An index file found in the same directory as the binary alignment\n map (BAM) file, a compressed binary version of a sequence alignment/map (SAM)\n file.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*.pairedMapped_sorted.bam.bai'\n exact_mappings:\n - NCIT:C190163\n\nURI: FilterTypeEnum
"},{"location":"FilterTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description particulate air filter None chemical air filter None low-MERV pleated media None HEPA None electrostatic None gas-phase or ultraviolet air treatments None"},{"location":"FilterTypeEnum/#slots","title":"Slots","text":"Name Description filter_type A device which removes solid particulates or airborne molecular contaminants"},{"location":"FilterTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FilterTypeEnum/#schema-source","title":"Schema Source","text":"name: filter_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n particulate air filter:\n text: particulate air filter\n chemical air filter:\n text: chemical air filter\n low-MERV pleated media:\n text: low-MERV pleated media\n HEPA:\n text: HEPA\n electrostatic:\n text: electrostatic\n gas-phase or ultraviolet air treatments:\n text: gas-phase or ultraviolet air treatments\n\nThe process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.
URI: nmdc:FiltrationProcess
classDiagram\n class FiltrationProcess\n click FiltrationProcess href \"../FiltrationProcess\"\n MaterialProcessing <|-- FiltrationProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n FiltrationProcess : alternative_identifiers\n\n FiltrationProcess : conditionings\n\n FiltrationProcess : container_size\n\n FiltrationProcess --> \"0..1\" QuantityValue : container_size\n click QuantityValue href \"../QuantityValue\"\n\n FiltrationProcess : description\n\n FiltrationProcess : end_date\n\n FiltrationProcess : filter_material\n\n FiltrationProcess : filter_pore_size\n\n FiltrationProcess --> \"0..1\" QuantityValue : filter_pore_size\n click QuantityValue href \"../QuantityValue\"\n\n FiltrationProcess : filtration_category\n\n FiltrationProcess : has_failure_categorization\n\n FiltrationProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n FiltrationProcess : has_input\n\n FiltrationProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n FiltrationProcess : has_output\n\n FiltrationProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n FiltrationProcess : id\n\n FiltrationProcess : instrument_used\n\n FiltrationProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n FiltrationProcess : is_pressurized\n\n FiltrationProcess : name\n\n FiltrationProcess : processing_institution\n\n FiltrationProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n FiltrationProcess : protocol_link\n\n FiltrationProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n FiltrationProcess : qc_comment\n\n FiltrationProcess : qc_status\n\n FiltrationProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n FiltrationProcess : separation_method\n\n FiltrationProcess --> \"0..1\" SeparationMethodEnum : separation_method\n click SeparationMethodEnum href \"../SeparationMethodEnum\"\n\n FiltrationProcess : start_date\n\n FiltrationProcess : type\n\n FiltrationProcess : volume\n\n FiltrationProcess --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: FiltrationProcess\ndescription: The process of segregation of phases; e.g. the separation of suspended\n solids from a liquid or gas, usually by forcing a carrier gas or liquid through\n a porous medium.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- CHMO:0001640\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslots:\n- conditionings\n- container_size\n- filter_material\n- filter_pore_size\n- filtration_category\n- is_pressurized\n- separation_method\n- volume\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The volume of sample filtered.\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:FiltrationProcess\n\nname: FiltrationProcess\ndescription: The process of segregation of phases; e.g. the separation of suspended\n solids from a liquid or gas, usually by forcing a carrier gas or liquid through\n a porous medium.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- CHMO:0001640\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The volume of sample filtered.\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n conditionings:\n name: conditionings\n description: Preliminary treatment of either phase with a suitable solution of\n the other phase (in the absence of main extractable solute(s)) so that when\n the subsequent equilibration is carried out changes in the (volume) phase ratio\n or in the concentrations of other components are minimized.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n list_elements_ordered: true\n alias: conditionings\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: string\n multivalued: true\n container_size:\n name: container_size\n description: The volume of the container an analyte is stored in or an activity\n takes place in\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: container_size\n owner: FiltrationProcess\n domain_of:\n - SubSamplingProcess\n - FiltrationProcess\n range: QuantityValue\n filter_material:\n name: filter_material\n description: A porous material on which solid particles present in air or other\n fluid which flows through it are largely caught and retained.\n comments:\n - 'Filters are made with a variety of materials: cellulose and derivatives, glass\n fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous\n or be made so by mechanical or other means. Membrane/ceramic filters are prepared\n with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene,\n polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement.\n The pores constitute 80\u201385% of the filter volume commonly and several pore sizes\n are available for air sampling (0.45\u22120.8 \u03bcm are commonly employed).'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: filter_material\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: string\n filter_pore_size:\n name: filter_pore_size\n description: A quantitative or qualitative measurement of the physical dimensions\n of the pores in a material.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: filter_pore_size\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: QuantityValue\n filtration_category:\n name: filtration_category\n description: The type of conditioning applied to a filter, device, etc.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: filtration_category\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: string\n is_pressurized:\n name: is_pressurized\n description: Whether or not pressure was applied to a thing or process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_pressurized\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: boolean\n separation_method:\n name: separation_method\n description: The method that was used to separate a substance from a solution\n or mixture.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: separation_method\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: SeparationMethodEnum\n volume:\n name: volume\n description: The volume of sample filtered.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: FiltrationProcess\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: FiltrationProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: FiltrationProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FiltrationProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FiltrationProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: FiltrationProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FiltrationProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FiltrationProcess\n\nA real number that conforms to the xsd:float specification
URI: xsd:float
base: float
uri: xsd:float
URI: FloorCondEnum
"},{"location":"FloorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"FloorCondEnum/#slots","title":"Slots","text":"Name Description floor_cond The physical condition of the floor at the time of sampling; photos or video ..."},{"location":"FloorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorCondEnum/#schema-source","title":"Schema Source","text":"name: floor_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nURI: FloorFinishMatEnum
"},{"location":"FloorFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description tile None wood strip or parquet None carpet None rug None laminate wood None lineoleum None vinyl composition tile None sheet vinyl None stone None bamboo None cork None terrazo None concrete None none None sealed None clear finish None paint None none or unfinished None"},{"location":"FloorFinishMatEnum/#slots","title":"Slots","text":"Name Description floor_finish_mat The floor covering type; the finished surface that is walked on"},{"location":"FloorFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorFinishMatEnum/#schema-source","title":"Schema Source","text":"name: floor_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n tile:\n text: tile\n wood strip or parquet:\n text: wood strip or parquet\n carpet:\n text: carpet\n rug:\n text: rug\n laminate wood:\n text: laminate wood\n lineoleum:\n text: lineoleum\n vinyl composition tile:\n text: vinyl composition tile\n sheet vinyl:\n text: sheet vinyl\n stone:\n text: stone\n bamboo:\n text: bamboo\n cork:\n text: cork\n terrazo:\n text: terrazo\n concrete:\n text: concrete\n none:\n text: none\n sealed:\n text: sealed\n clear finish:\n text: clear finish\n paint:\n text: paint\n none or unfinished:\n text: none or unfinished\n\nURI: FloorStrucEnum
"},{"location":"FloorStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description balcony None floating floor None glass floor None raised floor None sprung floor None wood-framed None concrete None"},{"location":"FloorStrucEnum/#slots","title":"Slots","text":"Name Description floor_struc Refers to the structural elements and subfloor upon which the finish flooring..."},{"location":"FloorStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorStrucEnum/#schema-source","title":"Schema Source","text":"name: floor_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n balcony:\n text: balcony\n floating floor:\n text: floating floor\n glass floor:\n text: glass floor\n raised floor:\n text: raised floor\n sprung floor:\n text: sprung floor\n wood-framed:\n text: wood-framed\n concrete:\n text: concrete\n\nURI: FloorWaterMoldEnum
"},{"location":"FloorWaterMoldEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mold odor None wet floor None water stains None wall discoloration None floor discoloration None ceiling discoloration None peeling paint or wallpaper None bulging walls None condensation None"},{"location":"FloorWaterMoldEnum/#slots","title":"Slots","text":"Name Description floor_water_mold Signs of the presence of mold or mildew in a room"},{"location":"FloorWaterMoldEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorWaterMoldEnum/#schema-source","title":"Schema Source","text":"name: floor_water_mold_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n mold odor:\n text: mold odor\n wet floor:\n text: wet floor\n water stains:\n text: water stains\n wall discoloration:\n text: wall discoloration\n floor discoloration:\n text: floor discoloration\n ceiling discoloration:\n text: ceiling discoloration\n peeling paint or wallpaper:\n text: peeling paint or wallpaper\n bulging walls:\n text: bulging walls\n condensation:\n text: condensation\n\nURI: FreqCleanEnum
"},{"location":"FreqCleanEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Daily None Weekly None Monthly None Quarterly None Annually None other None"},{"location":"FreqCleanEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FreqCleanEnum/#schema-source","title":"Schema Source","text":"name: freq_clean_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Daily:\n text: Daily\n Weekly:\n text: Weekly\n Monthly:\n text: Monthly\n Quarterly:\n text: Quarterly\n Annually:\n text: Annually\n other:\n text: other\n\nAn assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods
URI: nmdc:FunctionalAnnotation
classDiagram\n class FunctionalAnnotation\n click FunctionalAnnotation href \"../FunctionalAnnotation\"\n\n FunctionalAnnotation : feature_category\n\n FunctionalAnnotation --> \"0..1\" ControlledIdentifiedTermValue : feature_category\n click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n FunctionalAnnotation : has_function\n\n FunctionalAnnotation : subject\n\n FunctionalAnnotation --> \"0..1\" GeneProduct : subject\n click GeneProduct href \"../GeneProduct\"\n\n FunctionalAnnotation : type\n\n FunctionalAnnotation : was_generated_by\n\n FunctionalAnnotation --> \"0..1\" MetagenomeAnnotation : was_generated_by\n click MetagenomeAnnotation href \"../MetagenomeAnnotation\"\n\n\n\nname: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n by a gene product, or which the gene product plays an active role in. Functional\n annotations can be assigned manually by curators, or automatically in workflows. In\n the context of NMDC, all function annotation is performed automatically, typically\n using HMM or Blast type methods\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslots:\n- has_function\n- subject\n- was_generated_by\n- type\n- feature_category\nslot_usage:\n has_function:\n name: has_function\n notes:\n - Still missing patterns for COG and RetroRules\n - These patterns are not yet tied to the listed prefixes. A discussion about that\n possibility had been started, including the question of whether these lists\n are intended to be open examples or closed\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n range: MetagenomeAnnotation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\nclass_uri: nmdc:FunctionalAnnotation\n\nname: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n by a gene product, or which the gene product plays an active role in. Functional\n annotations can be assigned manually by curators, or automatically in workflows. In\n the context of NMDC, all function annotation is performed automatically, typically\n using HMM or Blast type methods\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslot_usage:\n has_function:\n name: has_function\n notes:\n - Still missing patterns for COG and RetroRules\n - These patterns are not yet tied to the listed prefixes. A discussion about that\n possibility had been started, including the question of whether these lists\n are intended to be open examples or closed\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n range: MetagenomeAnnotation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\nattributes:\n has_function:\n name: has_function\n notes:\n - Still missing patterns for COG and RetroRules\n - These patterns are not yet tied to the listed prefixes. A discussion about that\n possibility had been started, including the question of whether these lists\n are intended to be open examples or closed\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_function\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotation\n range: string\n pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n subject:\n name: subject\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: subject\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotation\n - OntologyRelation\n range: GeneProduct\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotationAggMember\n - FunctionalAnnotation\n - DataObject\n range: MetagenomeAnnotation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n any_of:\n - range: WorkflowExecution\n - range: DataGeneration\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FunctionalAnnotation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n feature_category:\n name: feature_category\n description: A Sequence Ontology term that describes the category of a feature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: feature_category\n owner: FunctionalAnnotation\n domain_of:\n - GenomeFeature\n - FunctionalAnnotation\n range: ControlledIdentifiedTermValue\nclass_uri: nmdc:FunctionalAnnotation\n\nURI: nmdc:FunctionalAnnotationAggMember
classDiagram\n class FunctionalAnnotationAggMember\n click FunctionalAnnotationAggMember href \"../FunctionalAnnotationAggMember\"\n\n FunctionalAnnotationAggMember : count\n\n FunctionalAnnotationAggMember : gene_function_id\n\n FunctionalAnnotationAggMember : type\n\n FunctionalAnnotationAggMember : was_generated_by\n\n FunctionalAnnotationAggMember --> \"1\" WorkflowExecution : was_generated_by\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\nname: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- was_generated_by\n- gene_function_id\n- count\n- type\nslot_usage:\n was_generated_by:\n name: was_generated_by\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan|wfmp|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n count:\n name: count\n description: The number of sequences (for a metagenome or metatranscriptome) or\n spectra (for metaproteomics) associated with the specified function.\nclass_uri: nmdc:FunctionalAnnotationAggMember\n\nname: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n was_generated_by:\n name: was_generated_by\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan|wfmp|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n count:\n name: count\n description: The number of sequences (for a metagenome or metatranscriptome) or\n spectra (for metaproteomics) associated with the specified function.\nattributes:\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n - FunctionalAnnotation\n - DataObject\n range: WorkflowExecution\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan|wfmp|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n any_of:\n - range: WorkflowExecution\n - range: DataGeneration\n gene_function_id:\n name: gene_function_id\n description: The identifier for the gene function.\n examples:\n - value: KEGG.ORTHOLOGY:K00627\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gene_function_id\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: uriorcurie\n required: true\n count:\n name: count\n description: The number of sequences (for a metagenome or metatranscriptome) or\n spectra (for metaproteomics) associated with the specified function.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: count\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: integer\n required: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FunctionalAnnotationAggMember\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FunctionalAnnotationAggMember\n\nAbstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:FunctionalAnnotationTerm
classDiagram\n class FunctionalAnnotationTerm\n click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n OntologyClass <|-- FunctionalAnnotationTerm\n click OntologyClass href \"../OntologyClass\"\n\n\n FunctionalAnnotationTerm <|-- Pathway\n click Pathway href \"../Pathway\"\n FunctionalAnnotationTerm <|-- OrthologyGroup\n click OrthologyGroup href \"../OrthologyGroup\"\n\n\n\n FunctionalAnnotationTerm : alternative_identifiers\n\n FunctionalAnnotationTerm : alternative_names\n\n FunctionalAnnotationTerm : definition\n\n FunctionalAnnotationTerm : description\n\n FunctionalAnnotationTerm : id\n\n FunctionalAnnotationTerm : name\n\n FunctionalAnnotationTerm : relations\n\n FunctionalAnnotationTerm --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n FunctionalAnnotationTerm : type\n\n\n\nname: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming (Duncan, 2021-04-02)\n- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup\n subclasses.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nclass_uri: nmdc:FunctionalAnnotationTerm\n\nname: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming (Duncan, 2021-04-02)\n- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup\n subclasses.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nattributes:\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: FunctionalAnnotationTerm\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: FunctionalAnnotationTerm\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: FunctionalAnnotationTerm\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: FunctionalAnnotationTerm\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FunctionalAnnotationTerm\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FunctionalAnnotationTerm\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: FunctionalAnnotationTerm\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FunctionalAnnotationTerm\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FunctionalAnnotationTerm\n\nURI: FurnitureEnum
"},{"location":"FurnitureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None chair None desks None"},{"location":"FurnitureEnum/#slots","title":"Slots","text":"Name Description furniture The types of furniture present in the sampled room"},{"location":"FurnitureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FurnitureEnum/#schema-source","title":"Schema Source","text":"name: furniture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cabinet:\n text: cabinet\n chair:\n text: chair\n desks:\n text: desks\n\nURI: GenderRestroomEnum
"},{"location":"GenderRestroomEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description all gender None female None gender neurtral None male None male and female None unisex None"},{"location":"GenderRestroomEnum/#slots","title":"Slots","text":"Name Description gender_restroom The gender type of the restroom"},{"location":"GenderRestroomEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GenderRestroomEnum/#schema-source","title":"Schema Source","text":"name: gender_restroom_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n all gender:\n text: all gender\n female:\n text: female\n gender neurtral:\n text: gender neurtral\n male:\n text: male\n male and female:\n text: male and female\n unisex:\n text: unisex\n\nA molecule encoded by a gene that has an evolved function
URI: nmdc:GeneProduct
classDiagram\n class GeneProduct\n click GeneProduct href \"../GeneProduct\"\n NamedThing <|-- GeneProduct\n click NamedThing href \"../NamedThing\"\n\n\n\n GeneProduct : alternative_identifiers\n\n GeneProduct : description\n\n GeneProduct : id\n\n GeneProduct : name\n\n GeneProduct : type\n\n\n\nInstances of this class should have identifiers with one of the following prefixes:
PR
UniProtKB
gtpo
name: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nclass_uri: nmdc:GeneProduct\n\nname: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: GeneProduct\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: GeneProduct\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: GeneProduct\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: GeneProduct\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: GeneProduct\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:GeneProduct\n\nA feature localized to an interval along a genome
URI: nmdc:GenomeFeature
classDiagram\n class GenomeFeature\n click GenomeFeature href \"../GenomeFeature\"\n\n GenomeFeature : encodes\n\n GenomeFeature --> \"0..1\" GeneProduct : encodes\n click GeneProduct href \"../GeneProduct\"\n\n GenomeFeature : end\n\n GenomeFeature : feature_category\n\n GenomeFeature --> \"0..1\" ControlledIdentifiedTermValue : feature_category\n click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n GenomeFeature : feature_type\n\n GenomeFeature : phase\n\n GenomeFeature : seqid\n\n GenomeFeature : start\n\n GenomeFeature : strand\n\n GenomeFeature : type\n\n\n\nname: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslots:\n- encodes\n- end\n- feature_type\n- phase\n- seqid\n- start\n- strand\n- type\n- feature_category\nslot_usage:\n seqid:\n name: seqid\n required: true\n start:\n name: start\n required: true\n end:\n name: end\n required: true\nclass_uri: nmdc:GenomeFeature\n\nname: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslot_usage:\n seqid:\n name: seqid\n required: true\n start:\n name: start\n required: true\n end:\n name: end\n required: true\nattributes:\n encodes:\n name: encodes\n description: The gene product encoded by this feature. Typically this is used\n for a CDS feature or gene feature which will encode a protein. It can also be\n used by a nc transcript ot gene feature that encoded a ncRNA\n todos:\n - If we revert Reaction back into the schema, that would be a reasonable domain\n for this slot\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: encodes\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: GeneProduct\n end:\n name: end\n description: The end of the feature in positive 1-based integer coordinates\n comments:\n - '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n feature, end = the position of the end + the length of the landmark feature.\"'\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - biolink:end_interbase_coordinate\n rank: 1000\n is_a: gff_coordinate\n alias: end\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n required: true\n minimum_value: 1\n feature_type:\n name: feature_type\n description: 'TODO: Yuri to write'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: feature_type\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n phase:\n name: phase\n description: The phase for a coding sequence entity. For example, phase of a CDS\n as represented in a GFF3 with a value of 0, 1 or 2.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - biolink:phase\n rank: 1000\n alias: phase\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n minimum_value: 0\n maximum_value: 2\n seqid:\n name: seqid\n description: The ID of the landmark used to establish the coordinate system for\n the current feature.\n todos:\n - change range from string to object\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: seqid\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n required: true\n start:\n name: start\n description: The start of the feature in positive 1-based integer coordinates\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - biolink:start_interbase_coordinate\n rank: 1000\n is_a: gff_coordinate\n alias: start\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n required: true\n minimum_value: 1\n strand:\n name: strand\n description: The strand on which a feature is located. Has a value of '+' (sense\n strand or forward strand) or '-' (anti-sense strand or reverse strand).\n todos:\n - set the range to an enum?\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - biolink:strand\n rank: 1000\n alias: strand\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: GenomeFeature\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n feature_category:\n name: feature_category\n description: A Sequence Ontology term that describes the category of a feature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: feature_category\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n - FunctionalAnnotation\n range: ControlledIdentifiedTermValue\nclass_uri: nmdc:GenomeFeature\n\nA normalized value for a location on the earth's surface
URI: nmdc:GeolocationValue
classDiagram\n class GeolocationValue\n click GeolocationValue href \"../GeolocationValue\"\n AttributeValue <|-- GeolocationValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n GeolocationValue : has_raw_value\n\n GeolocationValue : latitude\n\n GeolocationValue : longitude\n\n GeolocationValue : type\n\n\n\nname: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslots:\n- latitude\n- longitude\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n latitude:\n name: latitude\n required: true\n longitude:\n name: longitude\n required: true\nclass_uri: nmdc:GeolocationValue\n\nname: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n latitude:\n name: latitude\n required: true\n longitude:\n name: longitude\n required: true\nattributes:\n latitude:\n name: latitude\n description: latitude\n examples:\n - value: '-33.460524'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - schema:latitude\n rank: 1000\n slot_uri: wgs84:lat\n alias: latitude\n owner: GeolocationValue\n domain_of:\n - GeolocationValue\n range: decimal_degree\n required: true\n longitude:\n name: longitude\n description: longitude\n examples:\n - value: '150.168149'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - schema:longitude\n rank: 1000\n slot_uri: wgs84:long\n alias: longitude\n owner: GeolocationValue\n domain_of:\n - GeolocationValue\n range: decimal_degree\n required: true\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: GeolocationValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: GeolocationValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:GeolocationValue\n\nURI: GrowthHabitEnum
"},{"location":"GrowthHabitEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description erect None semi-erect None spreading None prostrate None"},{"location":"GrowthHabitEnum/#slots","title":"Slots","text":"Name Description growth_habit Characteristic shape, appearance or growth form of a plant species"},{"location":"GrowthHabitEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GrowthHabitEnum/#schema-source","title":"Schema Source","text":"name: growth_habit_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n erect:\n text: erect\n semi-erect:\n text: semi-erect\n spreading:\n text: spreading\n prostrate:\n text: prostrate\n\nURI: HandidnessEnum
"},{"location":"HandidnessEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ambidexterity None left handedness None mixed-handedness None right handedness None"},{"location":"HandidnessEnum/#slots","title":"Slots","text":"Name Description handidness The handidness of the individual sampled"},{"location":"HandidnessEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HandidnessEnum/#schema-source","title":"Schema Source","text":"name: handidness_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n ambidexterity:\n text: ambidexterity\n left handedness:\n text: left handedness\n mixed-handedness:\n text: mixed-handedness\n right handedness:\n text: right handedness\n\nURI: HcProducedEnum
"},{"location":"HcProducedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil None Gas-Condensate None Gas None Bitumen None Coalbed Methane None other None"},{"location":"HcProducedEnum/#slots","title":"Slots","text":"Name Description hc_produced Main hydrocarbon type produced from resource (i"},{"location":"HcProducedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcProducedEnum/#schema-source","title":"Schema Source","text":"name: hc_produced_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Oil:\n text: Oil\n Gas-Condensate:\n text: Gas-Condensate\n Gas:\n text: Gas\n Bitumen:\n text: Bitumen\n Coalbed Methane:\n text: Coalbed Methane\n other:\n text: other\n\nURI: HcrEnum
"},{"location":"HcrEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil Reservoir None Gas Reservoir None Oil Sand None Coalbed None Shale None Tight Oil Reservoir None Tight Gas Reservoir None other None"},{"location":"HcrEnum/#slots","title":"Slots","text":"Name Description hcr Main Hydrocarbon Resource type"},{"location":"HcrEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrEnum/#schema-source","title":"Schema Source","text":"name: hcr_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Oil Reservoir:\n text: Oil Reservoir\n Gas Reservoir:\n text: Gas Reservoir\n Oil Sand:\n text: Oil Sand\n Coalbed:\n text: Coalbed\n Shale:\n text: Shale\n Tight Oil Reservoir:\n text: Tight Oil Reservoir\n Tight Gas Reservoir:\n text: Tight Gas Reservoir\n other:\n text: other\n\nURI: HcrGeolAgeEnum
"},{"location":"HcrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"HcrGeolAgeEnum/#slots","title":"Slots","text":"Name Description hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en"},{"location":"HcrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrGeolAgeEnum/#schema-source","title":"Schema Source","text":"name: hcr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Archean:\n text: Archean\n Cambrian:\n text: Cambrian\n Carboniferous:\n text: Carboniferous\n Cenozoic:\n text: Cenozoic\n Cretaceous:\n text: Cretaceous\n Devonian:\n text: Devonian\n Jurassic:\n text: Jurassic\n Mesozoic:\n text: Mesozoic\n Neogene:\n text: Neogene\n Ordovician:\n text: Ordovician\n Paleogene:\n text: Paleogene\n Paleozoic:\n text: Paleozoic\n Permian:\n text: Permian\n Precambrian:\n text: Precambrian\n Proterozoic:\n text: Proterozoic\n Silurian:\n text: Silurian\n Triassic:\n text: Triassic\n other:\n text: other\n\nURI: HeatCoolTypeEnum
"},{"location":"HeatCoolTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description radiant system None heat pump None forced air system None steam forced heat None wood stove None"},{"location":"HeatCoolTypeEnum/#slots","title":"Slots","text":"Name Description heat_cool_type Methods of conditioning or heating a room or building"},{"location":"HeatCoolTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatCoolTypeEnum/#schema-source","title":"Schema Source","text":"name: heat_cool_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n radiant system:\n text: radiant system\n heat pump:\n text: heat pump\n forced air system:\n text: forced air system\n steam forced heat:\n text: steam forced heat\n wood stove:\n text: wood stove\n\nURI: HeatDelivLocEnum
"},{"location":"HeatDelivLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"HeatDelivLocEnum/#slots","title":"Slots","text":"Name Description heat_deliv_loc The location of heat delivery within the room"},{"location":"HeatDelivLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatDelivLocEnum/#schema-source","title":"Schema Source","text":"name: heat_deliv_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: HostSexEnum
"},{"location":"HostSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description female None hermaphrodite None non-binary None male None transgender None transgender (female to male) None transgender (male to female) None undeclared None"},{"location":"HostSexEnum/#slots","title":"Slots","text":"Name Description host_sex Gender or physical sex of the host"},{"location":"HostSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HostSexEnum/#schema-source","title":"Schema Source","text":"name: host_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n female:\n text: female\n hermaphrodite:\n text: hermaphrodite\n non-binary:\n text: non-binary\n male:\n text: male\n transgender:\n text: transgender\n transgender (female to male):\n text: transgender (female to male)\n transgender (male to female):\n text: transgender (male to female)\n undeclared:\n text: undeclared\n\nAn attribute value representing an image.
URI: nmdc:ImageValue
classDiagram\n class ImageValue\n click ImageValue href \"../ImageValue\"\n AttributeValue <|-- ImageValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n ImageValue : description\n\n ImageValue : display_order\n\n ImageValue : has_raw_value\n\n ImageValue : type\n\n ImageValue : url\n\n\n\nname: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- url\n- description\n- display_order\nclass_uri: nmdc:ImageValue\n\nname: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: url\n owner: ImageValue\n domain_of:\n - ImageValue\n - Protocol\n - DataObject\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ImageValue\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n display_order:\n name: display_order\n description: When rendering information, this attribute to specify the order in\n which the information should be rendered.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: display_order\n owner: ImageValue\n domain_of:\n - ImageValue\n range: integer\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: ImageValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ImageValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ImageValue\n\nURI: IndoorSpaceEnum
"},{"location":"IndoorSpaceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bedroom None office None bathroom None foyer None kitchen None locker room None hallway None elevator None"},{"location":"IndoorSpaceEnum/#slots","title":"Slots","text":"Name Description indoor_space A distinguishable space within a structure, the purpose for which discrete ar..."},{"location":"IndoorSpaceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSpaceEnum/#schema-source","title":"Schema Source","text":"name: indoor_space_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bedroom:\n text: bedroom\n office:\n text: office\n bathroom:\n text: bathroom\n foyer:\n text: foyer\n kitchen:\n text: kitchen\n locker room:\n text: locker room\n hallway:\n text: hallway\n elevator:\n text: elevator\n\nURI: IndoorSurfEnum
"},{"location":"IndoorSurfEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None ceiling None counter top None door None shelving None vent cover None window None wall None"},{"location":"IndoorSurfEnum/#slots","title":"Slots","text":"Name Description indoor_surf Type of indoor surface"},{"location":"IndoorSurfEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSurfEnum/#schema-source","title":"Schema Source","text":"name: indoor_surf_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cabinet:\n text: cabinet\n ceiling:\n text: ceiling\n counter top:\n text: counter top\n door:\n text: door\n shelving:\n text: shelving\n vent cover:\n text: vent cover\n window:\n text: window\n wall:\n text: wall\n\nAny data or knowledge that reduces uncertainty or enhances understanding about a system, process, or entity.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:InformationObject
classDiagram\n class InformationObject\n click InformationObject href \"../InformationObject\"\n NamedThing <|-- InformationObject\n click NamedThing href \"../NamedThing\"\n\n\n InformationObject <|-- Configuration\n click Configuration href \"../Configuration\"\n InformationObject <|-- Manifest\n click Manifest href \"../Manifest\"\n InformationObject <|-- CalibrationInformation\n click CalibrationInformation href \"../CalibrationInformation\"\n InformationObject <|-- DataObject\n click DataObject href \"../DataObject\"\n\n\n\n InformationObject : alternative_identifiers\n\n InformationObject : description\n\n InformationObject : id\n\n InformationObject : name\n\n InformationObject : type\n\n\n\nname: InformationObject\ndescription: Any data or knowledge that reduces uncertainty or enhances understanding\n about a system, process, or entity.\ncomments:\n- The direct subclasses of NamedThing should aggregate the relevant classes and make\n them uniform. PlannedProcess and MaterialEntity are clearly disjoint. Let's do the\n same thing for our modelling of things that don't consist of matter and aren't processes.\n- InformationObjects may include embedded data or links to external resources via\n the url slot\n- May appear as output from a process, inputs into a process, or both\n- All slots relating one class to a InformationObject should be is_a sub-properties\n of has_input or has_output, if they are multivalued or otherwise organized\n- Historically information about many classes has been inlined into the class. This\n is an alternative pattern.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:AttributeValue\nis_a: NamedThing\nabstract: true\nclass_uri: nmdc:InformationObject\n\nname: InformationObject\ndescription: Any data or knowledge that reduces uncertainty or enhances understanding\n about a system, process, or entity.\ncomments:\n- The direct subclasses of NamedThing should aggregate the relevant classes and make\n them uniform. PlannedProcess and MaterialEntity are clearly disjoint. Let's do the\n same thing for our modelling of things that don't consist of matter and aren't processes.\n- InformationObjects may include embedded data or links to external resources via\n the url slot\n- May appear as output from a process, inputs into a process, or both\n- All slots relating one class to a InformationObject should be is_a sub-properties\n of has_input or has_output, if they are multivalued or otherwise organized\n- Historically information about many classes has been inlined into the class. This\n is an alternative pattern.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:AttributeValue\nis_a: NamedThing\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: InformationObject\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: InformationObject\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: InformationObject\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: InformationObject\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: InformationObject\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:InformationObject\n\nA material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
URI: nmdc:Instrument
classDiagram\n class Instrument\n click Instrument href \"../Instrument\"\n MaterialEntity <|-- Instrument\n click MaterialEntity href \"../MaterialEntity\"\n\n\n\n Instrument : alternative_identifiers\n\n Instrument : description\n\n Instrument : id\n\n Instrument : model\n\n Instrument --> \"0..1\" InstrumentModelEnum : model\n click InstrumentModelEnum href \"../InstrumentModelEnum\"\n\n Instrument : name\n\n Instrument : type\n\n Instrument : vendor\n\n Instrument --> \"0..1\" InstrumentVendorEnum : vendor\n click InstrumentVendorEnum href \"../InstrumentVendorEnum\"\n\n\n\nname: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n investigation, but is not a reagent.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000968\nis_a: MaterialEntity\nslots:\n- vendor\n- model\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:Instrument\n\nname: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n investigation, but is not a reagent.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000968\nis_a: MaterialEntity\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n vendor:\n name: vendor\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: vendor\n owner: Instrument\n domain_of:\n - Instrument\n range: InstrumentVendorEnum\n model:\n name: model\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: model\n owner: Instrument\n domain_of:\n - Instrument\n range: InstrumentModelEnum\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Instrument\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Instrument\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Instrument\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Instrument\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Instrument\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Instrument\n\nURI: InstrumentModelEnum
"},{"location":"InstrumentModelEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description exploris_21T None exploris_240 None exploris_480 None ltq_orbitrap_velos None orbitrap_fusion_lumos None orbitrap_eclipse_tribid None orbitrap_q_exactive None solarix_7T None solarix_12T None solarix_15T None agilent_8890A None agilent_7980A None vortex_genie_2 None novaseq None novaseq_6000 OBI:0002630 novaseq_x None hiseq None hiseq_1000 OBI:0002022 hiseq_1500 OBI:0003386 hiseq_2000 OBI:0002001 hiseq_2500 OBI:0002002 hiseq_3000 OBI:0002048 hiseq_4000 OBI:0002049 hiseq_x_ten OBI:0002129 miniseq OBI:0003114 miseq OBI:0002003 nextseq_1000 OBI:0003606 nextseq None nextseq_500 OBI:0002021 nextseq_550 OBI:0003387 gridion OBI:0002751 minion OBI:0002750 promethion OBI:0002752 rs_II OBI:0002012 sequel OBI:0002632 sequel_II OBI:0002633 revio None"},{"location":"InstrumentModelEnum/#slots","title":"Slots","text":"Name Description model"},{"location":"InstrumentModelEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InstrumentModelEnum/#schema-source","title":"Schema Source","text":"name: InstrumentModelEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n exploris_21T:\n text: exploris_21T\n aliases:\n - Exploris 21T\n exploris_240:\n text: exploris_240\n aliases:\n - Orbitrap Exploris 240\n exploris_480:\n text: exploris_480\n aliases:\n - Orbitrap Exploris 480\n ltq_orbitrap_velos:\n text: ltq_orbitrap_velos\n aliases:\n - LTQ Orbitrap Velos\n - LTQ Orbitrap Velos ETD\n - Velos\n orbitrap_fusion_lumos:\n text: orbitrap_fusion_lumos\n aliases:\n - Orbitrap Fusion Lumos\n - Fusion\n orbitrap_eclipse_tribid:\n text: orbitrap_eclipse_tribid\n aliases:\n - Orbitrap Eclipse Tribid\n - Eclipse\n orbitrap_q_exactive:\n text: orbitrap_q_exactive\n aliases:\n - Orbitrap Q-Exactive HF\n - Orbitrap Q-Exactive HF-X\n solarix_7T:\n text: solarix_7T\n aliases:\n - 7T Solarix\n - 7T FT-ICR MS\n - 7T MRMS\n solarix_12T:\n text: solarix_12T\n aliases:\n - 12T Solarix\n - 12T FT-ICR MS\n - 12T MRMS\n solarix_15T:\n text: solarix_15T\n aliases:\n - 15T Solarix\n - 15T FT-ICR MS\n - 15T MRMS\n agilent_8890A:\n text: agilent_8890A\n aliases:\n - 8890A GC-MS\n - Agilent GC MS\n agilent_7980A:\n text: agilent_7980A\n aliases:\n - 7980A GC-MS\n - Agilent GC MS\n vortex_genie_2:\n text: vortex_genie_2\n aliases:\n - VortexGenie2\n novaseq:\n text: novaseq\n aliases:\n - NovaSeq\n - Illumina NovaSeq\n novaseq_6000:\n text: novaseq_6000\n meaning: OBI:0002630\n comments:\n - Possible flowcell versions are SP, S1, S2, S4.\n see_also:\n - https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html\n aliases:\n - NovaSeq 6000\n - Illumina NovaSeq 6000\n structured_aliases:\n Illumina NovaSeq S2:\n literal_form: Illumina NovaSeq S2\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n Illumina NovaSeq S4:\n literal_form: Illumina NovaSeq S4\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n Illumina NovaSeq SP:\n literal_form: Illumina NovaSeq SP\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n novaseq_x:\n text: novaseq_x\n comments:\n - Possible flowcell versions are 1.5B, 10B, 25B. Only difference between X and\n X Plus is 2 flowcells for X Plus versus 1 flowcell for X.\n see_also:\n - https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html\n aliases:\n - Illumina NovaSeq X\n - Illumina NovaSeq X Plus\n hiseq:\n text: hiseq\n aliases:\n - Illumina HiSeq\n hiseq_1000:\n text: hiseq_1000\n meaning: OBI:0002022\n aliases:\n - Illumina HiSeq 1000\n hiseq_1500:\n text: hiseq_1500\n meaning: OBI:0003386\n aliases:\n - Illumina HiSeq 1500\n hiseq_2000:\n text: hiseq_2000\n meaning: OBI:0002001\n aliases:\n - Illumina HiSeq 2000\n hiseq_2500:\n text: hiseq_2500\n meaning: OBI:0002002\n aliases:\n - Illumina HiSeq 2500\n structured_aliases:\n Illumina HiSeq 2500-1TB:\n literal_form: Illumina HiSeq 2500-1TB\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n Illumina HiSeq 2500-Rapid:\n literal_form: Illumina HiSeq 2500-Rapid\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n hiseq_3000:\n text: hiseq_3000\n meaning: OBI:0002048\n aliases:\n - Illumina HiSeq 3000\n hiseq_4000:\n text: hiseq_4000\n meaning: OBI:0002049\n aliases:\n - Illumina HiSeq 4000\n hiseq_x_ten:\n text: hiseq_x_ten\n meaning: OBI:0002129\n aliases:\n - Illumina HiSeq X Ten\n miniseq:\n text: miniseq\n meaning: OBI:0003114\n aliases:\n - Illumina MiniSeq\n miseq:\n text: miseq\n meaning: OBI:0002003\n aliases:\n - MiSeq\n - Illumina MiSeq\n nextseq_1000:\n text: nextseq_1000\n meaning: OBI:0003606\n aliases:\n - Illumina NextSeq 1000\n nextseq:\n text: nextseq\n aliases:\n - NextSeq\n - Illumina NextSeq\n structured_aliases:\n Illumina NextSeq-HO:\n literal_form: Illumina NextSeq-HO\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n Illumina NextSeq-MO:\n literal_form: Illumina NextSeq-MO\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n nextseq_500:\n text: nextseq_500\n meaning: OBI:0002021\n aliases:\n - NextSeq 500\n - Illumina NextSeq 500\n nextseq_550:\n text: nextseq_550\n meaning: OBI:0003387\n aliases:\n - NextSeq 550\n - Illumina NextSeq 550\n gridion:\n text: gridion\n meaning: OBI:0002751\n aliases:\n - Oxford Nanopore GridION Mk1\n minion:\n text: minion\n meaning: OBI:0002750\n aliases:\n - Oxford Nanopore MinION\n promethion:\n text: promethion\n meaning: OBI:0002752\n aliases:\n - Oxford Nanopore PromethION\n rs_II:\n text: rs_II\n meaning: OBI:0002012\n aliases:\n - PacBio RS II\n sequel:\n text: sequel\n meaning: OBI:0002632\n aliases:\n - PacBio Sequel\n sequel_II:\n text: sequel_II\n meaning: OBI:0002633\n aliases:\n - PacBio Sequel II\n revio:\n text: revio\n aliases:\n - PacBio Revio\n - Revio\n\nURI: InstrumentVendorEnum
"},{"location":"InstrumentVendorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description waters None agilent None bruker None thermo_fisher None vwr None perkin_elmer None gilson None scientific_industries None illumina OBI:0000759 pacbio OBI:0001856 oxford_nanopore OBI:0002755 pnnl None"},{"location":"InstrumentVendorEnum/#slots","title":"Slots","text":"Name Description vendor"},{"location":"InstrumentVendorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InstrumentVendorEnum/#schema-source","title":"Schema Source","text":"name: InstrumentVendorEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n waters:\n text: waters\n aliases:\n - Waters Corporation\n agilent:\n text: agilent\n aliases:\n - Agilent Technologies\n bruker:\n text: bruker\n aliases:\n - Bruker Corporation\n - Bruker Daltonics\n thermo_fisher:\n text: thermo_fisher\n aliases:\n - ThermoFisher\n - Thermo Fisher Scientific\n vwr:\n text: vwr\n perkin_elmer:\n text: perkin_elmer\n gilson:\n text: gilson\n scientific_industries:\n text: scientific_industries\n illumina:\n text: illumina\n meaning: OBI:0000759\n aliases:\n - Illumina\n pacbio:\n text: pacbio\n meaning: OBI:0001856\n aliases:\n - PacBio\n - Pacific Biosciences\n oxford_nanopore:\n text: oxford_nanopore\n meaning: OBI:0002755\n aliases:\n - Oxford Nanopore Technologies\n pnnl:\n text: pnnl\n aliases:\n - PNNL\n\nURI: IntWallCondEnum
"},{"location":"IntWallCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"IntWallCondEnum/#slots","title":"Slots","text":"Name Description int_wall_cond The physical condition of the wall at the time of sampling; photos or video p..."},{"location":"IntWallCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IntWallCondEnum/#schema-source","title":"Schema Source","text":"name: int_wall_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nAn integer
URI: xsd:integer
base: int
uri: xsd:integer
URI: IonizationSourceEnum
"},{"location":"IonizationSourceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description electrospray_ionization None matrix_assisted_laser_desorption_ionization None atmospheric_pressure_photo_ionization None atmospheric_pressure_chemical_ionization None electron_ionization None"},{"location":"IonizationSourceEnum/#slots","title":"Slots","text":"Name Description ionization_source The ionization source used to introduce processed samples into a mass spectro..."},{"location":"IonizationSourceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IonizationSourceEnum/#schema-source","title":"Schema Source","text":"name: IonizationSourceEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n electrospray_ionization:\n text: electrospray_ionization\n aliases:\n - ESI\n matrix_assisted_laser_desorption_ionization:\n text: matrix_assisted_laser_desorption_ionization\n aliases:\n - MALDI\n atmospheric_pressure_photo_ionization:\n text: atmospheric_pressure_photo_ionization\n aliases:\n - APPI\n atmospheric_pressure_chemical_ionization:\n text: atmospheric_pressure_chemical_ionization\n aliases:\n - APCI\n electron_ionization:\n text: electron_ionization\n aliases:\n - EI\n\nURI: JgiContTypeEnum
"},{"location":"JgiContTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plate None tube None"},{"location":"JgiContTypeEnum/#slots","title":"Slots","text":"Name Description dna_cont_type Tube or plate (96-well) rna_cont_type Tube or plate (96-well)"},{"location":"JgiContTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"JgiContTypeEnum/#schema-source","title":"Schema Source","text":"name: JgiContTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n plate:\n text: plate\n tube:\n text: tube\n\nA string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A language code conforming to ISO_639-1
URI: xsd:language
base: str
uri: xsd:language
URI: nmdc:LibraryPreparation
classDiagram\n class LibraryPreparation\n click LibraryPreparation href \"../LibraryPreparation\"\n MaterialProcessing <|-- LibraryPreparation\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n LibraryPreparation : alternative_identifiers\n\n LibraryPreparation : description\n\n LibraryPreparation : end_date\n\n LibraryPreparation : has_failure_categorization\n\n LibraryPreparation --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n LibraryPreparation : has_input\n\n LibraryPreparation --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n LibraryPreparation : has_output\n\n LibraryPreparation --> \"1..*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n LibraryPreparation : id\n\n LibraryPreparation : instrument_used\n\n LibraryPreparation --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n LibraryPreparation : is_stranded\n\n LibraryPreparation : library_preparation_kit\n\n LibraryPreparation : library_type\n\n LibraryPreparation --> \"0..1\" LibraryTypeEnum : library_type\n click LibraryTypeEnum href \"../LibraryTypeEnum\"\n\n LibraryPreparation : name\n\n LibraryPreparation : nucl_acid_amp\n\n LibraryPreparation --> \"0..1\" TextValue : nucl_acid_amp\n click TextValue href \"../TextValue\"\n\n LibraryPreparation : pcr_cond\n\n LibraryPreparation --> \"0..1\" TextValue : pcr_cond\n click TextValue href \"../TextValue\"\n\n LibraryPreparation : pcr_cycles\n\n LibraryPreparation : pcr_primers\n\n LibraryPreparation --> \"0..1\" TextValue : pcr_primers\n click TextValue href \"../TextValue\"\n\n LibraryPreparation : processing_institution\n\n LibraryPreparation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n LibraryPreparation : protocol_link\n\n LibraryPreparation --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n LibraryPreparation : qc_comment\n\n LibraryPreparation : qc_status\n\n LibraryPreparation --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n LibraryPreparation : start_date\n\n LibraryPreparation : stranded_orientation\n\n LibraryPreparation --> \"0..1\" StrandedOrientationEnum : stranded_orientation\n click StrandedOrientationEnum href \"../StrandedOrientationEnum\"\n\n LibraryPreparation : type\n\n\n\nname: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: MaterialProcessing\nslots:\n- is_stranded\n- library_preparation_kit\n- library_type\n- nucl_acid_amp\n- pcr_cond\n- pcr_cycles\n- pcr_primers\n- stranded_orientation\nslot_usage:\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n interpolated: true\n pcr_cond:\n name: pcr_cond\n description: Description of reaction conditions and components of polymerase chain\n reaction performed during library preparation\nclass_uri: nmdc:LibraryPreparation\n\nname: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: MaterialProcessing\nslot_usage:\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n interpolated: true\n pcr_cond:\n name: pcr_cond\n description: Description of reaction conditions and components of polymerase chain\n reaction performed during library preparation\nattributes:\n is_stranded:\n name: is_stranded\n description: Is the (RNA) library stranded or non-stranded (unstranded).\n comments:\n - A value of true means the library is stranded, flase means non-stranded.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_stranded\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: boolean\n library_preparation_kit:\n name: library_preparation_kit\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: library_preparation_kit\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: string\n library_type:\n name: library_type\n title: library type\n examples:\n - value: DNA\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: library_type\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: LibraryTypeEnum\n nucl_acid_amp:\n name: nucl_acid_amp\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the enzymatic amplification (PCR,\n TMA, NASBA) of specific nucleic acids\n title: nucleic acid amplification\n examples:\n - value: https://phylogenomics.me/protocols/16s-pcr-protocol/\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid amplification\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000038\n alias: nucl_acid_amp\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: TextValue\n multivalued: false\n pcr_cond:\n name: pcr_cond\n annotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n description: Description of reaction conditions and components of polymerase chain\n reaction performed during library preparation\n title: pcr conditions\n examples:\n - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr conditions\n rank: 1000\n is_a: sequencing field\n string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n slot_uri: MIXS:0000049\n alias: pcr_cond\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: TextValue\n multivalued: false\n pcr_cycles:\n name: pcr_cycles\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - OBI:0002475\n rank: 1000\n alias: pcr_cycles\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: integer\n pcr_primers:\n name: pcr_primers\n annotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\n description: PCR primers that were used to amplify the sequence of the targeted\n gene, locus or subfragment. This field should contain all the primers used for\n a single PCR reaction if multiple forward or reverse primers are present in\n a single PCR reaction. The primer sequence should be reported in uppercase letters\n title: pcr primers\n examples:\n - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr primers\n rank: 1000\n is_a: sequencing field\n string_serialization: FWD:{dna};REV:{dna}\n slot_uri: MIXS:0000046\n alias: pcr_primers\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: TextValue\n multivalued: false\n stranded_orientation:\n name: stranded_orientation\n description: Lists the strand orientiation for a stranded RNA library preparation.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: stranded_orientation\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: StrandedOrientationEnum\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: LibraryPreparation\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: LibraryPreparation\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: LibraryPreparation\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: LibraryPreparation\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: LibraryPreparation\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: LibraryPreparation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:LibraryPreparation\n\nURI: LibraryTypeEnum
"},{"location":"LibraryTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None"},{"location":"LibraryTypeEnum/#slots","title":"Slots","text":"Name Description library_type"},{"location":"LibraryTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LibraryTypeEnum/#schema-source","title":"Schema Source","text":"name: LibraryTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DNA:\n text: DNA\n RNA:\n text: RNA\n\nURI: LightTypeEnum
"},{"location":"LightTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description natural light None electric light None desk lamp None flourescent lights None none None"},{"location":"LightTypeEnum/#slots","title":"Slots","text":"Name Description light_type Application of light to achieve some practical or aesthetic effect"},{"location":"LightTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LightTypeEnum/#schema-source","title":"Schema Source","text":"name: light_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n natural light:\n text: natural light\n electric light:\n text: electric light\n desk lamp:\n text: desk lamp\n flourescent lights:\n text: flourescent lights\n none:\n text: none\n\nURI: LithologyEnum
"},{"location":"LithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Basement None Chalk None Chert None Coal None Conglomerate None Diatomite None Dolomite None Limestone None Sandstone None Shale None Siltstone None Volcanic None other None"},{"location":"LithologyEnum/#slots","title":"Slots","text":"Name Description lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki"},{"location":"LithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LithologyEnum/#schema-source","title":"Schema Source","text":"name: lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Basement:\n text: Basement\n Chalk:\n text: Chalk\n Chert:\n text: Chert\n Coal:\n text: Coal\n Conglomerate:\n text: Conglomerate\n Diatomite:\n text: Diatomite\n Dolomite:\n text: Dolomite\n Limestone:\n text: Limestone\n Sandstone:\n text: Sandstone\n Shale:\n text: Shale\n Siltstone:\n text: Siltstone\n Volcanic:\n text: Volcanic\n other:\n text: other\n\nURI: nmdc:MagBin
classDiagram\n class MagBin\n click MagBin href \"../MagBin\"\n\n MagBin : bin_name\n\n MagBin : bin_quality\n\n MagBin --> \"0..1\" BinQualityEnum : bin_quality\n click BinQualityEnum href \"../BinQualityEnum\"\n\n MagBin : completeness\n\n MagBin : contamination\n\n MagBin : eukaryotic_evaluation\n\n MagBin --> \"0..1\" EukEval : eukaryotic_evaluation\n click EukEval href \"../EukEval\"\n\n MagBin : gene_count\n\n MagBin : gtdbtk_class\n\n MagBin : gtdbtk_domain\n\n MagBin : gtdbtk_family\n\n MagBin : gtdbtk_genus\n\n MagBin : gtdbtk_order\n\n MagBin : gtdbtk_phylum\n\n MagBin : gtdbtk_species\n\n MagBin : members_id\n\n MagBin : num_16s\n\n MagBin : num_23s\n\n MagBin : num_5s\n\n MagBin : num_t_rna\n\n MagBin : number_of_contig\n\n MagBin : total_bases\n\n MagBin : type\n\n\n\nname: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- bin_name\n- bin_quality\n- completeness\n- contamination\n- gene_count\n- gtdbtk_class\n- gtdbtk_domain\n- gtdbtk_family\n- gtdbtk_genus\n- gtdbtk_order\n- gtdbtk_phylum\n- gtdbtk_species\n- members_id\n- num_16s\n- num_23s\n- num_5s\n- num_t_rna\n- number_of_contig\n- total_bases\n- type\n- eukaryotic_evaluation\nclass_uri: nmdc:MagBin\n\nname: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n bin_name:\n name: bin_name\n description: Name of the metagenome-assembled genome.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bin_name\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n required: true\n bin_quality:\n name: bin_quality\n description: The quality of the metagenome-assembled genome based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bin_quality\n owner: MagBin\n domain_of:\n - MagBin\n range: BinQualityEnum\n completeness:\n name: completeness\n description: Estimate of the completeness of the metagenome-assembled genome,\n estimated by a tool like CheckM.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: completeness\n owner: MagBin\n domain_of:\n - EukEval\n - MagBin\n range: float\n minimum_value: 0\n contamination:\n name: contamination\n description: Estimate of the completeness of the metagenome-assembled genome,\n estimated by a tool like CheckM.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contamination\n owner: MagBin\n domain_of:\n - EukEval\n - MagBin\n range: float\n minimum_value: 0\n gene_count:\n name: gene_count\n description: Number of genes.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gene_count\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n gtdbtk_class:\n name: gtdbtk_class\n description: Taxonomic class assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:class\n rank: 1000\n alias: gtdbtk_class\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_domain:\n name: gtdbtk_domain\n description: Taxonomic domain assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:superkingdom\n rank: 1000\n alias: gtdbtk_domain\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_family:\n name: gtdbtk_family\n description: Taxonomic family assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:family\n rank: 1000\n alias: gtdbtk_family\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_genus:\n name: gtdbtk_genus\n description: Taxonomic genus assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:genus\n rank: 1000\n alias: gtdbtk_genus\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_order:\n name: gtdbtk_order\n description: Taxonomic order assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:order\n rank: 1000\n alias: gtdbtk_order\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_phylum:\n name: gtdbtk_phylum\n description: Taxonomic phylum assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:phylum\n rank: 1000\n alias: gtdbtk_phylum\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_species:\n name: gtdbtk_species\n description: Taxonomic genus assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:species\n rank: 1000\n alias: gtdbtk_species\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n members_id:\n name: members_id\n description: Names of the contigs that make up a metagenome-assembled genome.\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - GENEPIO:0100596\n rank: 1000\n alias: members_id\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n multivalued: true\n num_16s:\n name: num_16s\n description: Number of 16s sequences detected, a subunit of prokaryotic ribosomes.\n from_schema: https://w3id.org/nmdc/nmdc\n broad_mappings:\n - NCIT:C105370\n rank: 1000\n alias: num_16s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n num_23s:\n name: num_23s\n description: Number of 23 seqeuences detected, a subunit of ribosomes.\n from_schema: https://w3id.org/nmdc/nmdc\n broad_mappings:\n - OMIT:0013245\n rank: 1000\n alias: num_23s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n num_5s:\n name: num_5s\n description: Number of 5s seqeuences detected, a subunit of ribosomes.\n from_schema: https://w3id.org/nmdc/nmdc\n broad_mappings:\n - OMIT:0013248\n rank: 1000\n alias: num_5s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n num_t_rna:\n name: num_t_rna\n description: Number of transfer transfer RNAs.\n from_schema: https://w3id.org/nmdc/nmdc\n broad_mappings:\n - NCIT:C816\n rank: 1000\n alias: num_t_rna\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n number_of_contig:\n name: number_of_contig\n description: Number of contigs\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - GENEPIO:0000093\n rank: 1000\n alias: number_of_contig\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n total_bases:\n name: total_bases\n description: Total number of basepairs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: total_bases\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MagBin\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n eukaryotic_evaluation:\n name: eukaryotic_evaluation\n description: Contains results from evaluating if a Metagenome-Assembled Genome\n is of eukaryotic lineage.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: eukaryotic_evaluation\n owner: MagBin\n domain_of:\n - MagBin\n range: EukEval\nclass_uri: nmdc:MagBin\n\nA workflow execution activity that uses computational binning tools to group assembled contigs into genomes
URI: nmdc:MagsAnalysis
classDiagram\n class MagsAnalysis\n click MagsAnalysis href \"../MagsAnalysis\"\n WorkflowExecution <|-- MagsAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MagsAnalysis : alternative_identifiers\n\n MagsAnalysis : binned_contig_num\n\n MagsAnalysis : description\n\n MagsAnalysis : end_date\n\n MagsAnalysis : ended_at_time\n\n MagsAnalysis : execution_resource\n\n MagsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MagsAnalysis : git_url\n\n MagsAnalysis : has_failure_categorization\n\n MagsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MagsAnalysis : has_input\n\n MagsAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MagsAnalysis : has_output\n\n MagsAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MagsAnalysis : id\n\n MagsAnalysis : img_identifiers\n\n MagsAnalysis : input_contig_num\n\n MagsAnalysis : low_depth_contig_num\n\n MagsAnalysis : mags_list\n\n MagsAnalysis --> \"*\" MagBin : mags_list\n click MagBin href \"../MagBin\"\n\n MagsAnalysis : name\n\n MagsAnalysis : processing_institution\n\n MagsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MagsAnalysis : protocol_link\n\n MagsAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MagsAnalysis : qc_comment\n\n MagsAnalysis : qc_status\n\n MagsAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MagsAnalysis : start_date\n\n MagsAnalysis : started_at_time\n\n MagsAnalysis : too_short_contig_num\n\n MagsAnalysis : type\n\n MagsAnalysis : unbinned_contig_num\n\n MagsAnalysis : version\n\n MagsAnalysis : was_informed_by\n\n MagsAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MagsAnalysis\ndescription: A workflow execution activity that uses computational binning tools to\n group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- binned_contig_num\n- input_contig_num\n- low_depth_contig_num\n- mags_list\n- too_short_contig_num\n- unbinned_contig_num\n- img_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MagsAnalysis\n\nname: MagsAnalysis\ndescription: A workflow execution activity that uses computational binning tools to\n group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n binned_contig_num:\n name: binned_contig_num\n description: Number of contigs that ended up in a medium or high quality bin.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: binned_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n input_contig_num:\n name: input_contig_num\n description: Total number of input contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: input_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n low_depth_contig_num:\n name: low_depth_contig_num\n description: Number of contigs which were excluded from binning for depth of coverage.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: low_depth_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n mags_list:\n name: mags_list\n description: Contains detailed information about each metagenome-assembled genome.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mags_list\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: MagBin\n multivalued: true\n inlined: true\n inlined_as_list: true\n too_short_contig_num:\n name: too_short_contig_num\n description: Number of contigs which were excluded from binning for length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: too_short_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n unbinned_contig_num:\n name: unbinned_contig_num\n description: Number of contigs which did not end up in a medium or high quality\n bin.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: unbinned_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: MagsAnalysis\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n maximum_cardinality: 1\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MagsAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MagsAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MagsAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MagsAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MagsAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MagsAnalysis\n\nA qualified collection of DataObjects that can be analyzed together in the same experimental context.
URI: nmdc:Manifest
classDiagram\n class Manifest\n click Manifest href \"../Manifest\"\n InformationObject <|-- Manifest\n click InformationObject href \"../InformationObject\"\n\n\n\n Manifest : alternative_identifiers\n\n Manifest : description\n\n Manifest : id\n\n Manifest : manifest_category\n\n Manifest --> \"1\" ManifestCategoryEnum : manifest_category\n click ManifestCategoryEnum href \"../ManifestCategoryEnum\"\n\n Manifest : name\n\n Manifest : type\n\n\n\nname: Manifest\ndescription: A qualified collection of DataObjects that can be analyzed together in\n the same experimental context.\ncomments:\n- Manifest are currently uncoupled from other modelling. For example, there is no\n schema requirement that DataObjects in a fractions Manifest were all obtained by\n analyzing the same ProcessedSample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- manifest_category\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\nclass_uri: nmdc:Manifest\n\nname: Manifest\ndescription: A qualified collection of DataObjects that can be analyzed together in\n the same experimental context.\ncomments:\n- Manifest are currently uncoupled from other modelling. For example, there is no\n schema requirement that DataObjects in a fractions Manifest were all obtained by\n analyzing the same ProcessedSample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\nattributes:\n manifest_category:\n name: manifest_category\n description: The type of context in which the constituent DataObjects can be analyzed\n together.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: manifest_category\n owner: Manifest\n domain_of:\n - Manifest\n range: ManifestCategoryEnum\n required: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Manifest\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Manifest\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Manifest\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Manifest\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Manifest\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Manifest\n\nA list of contexts in which some DataObjects can be analyzed together.
URI: ManifestCategoryEnum
"},{"location":"ManifestCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description instrument_run None A collection of data objects from a single run of an instrument poolable_replicates None A collection of data objects that can be pooled for downstream analyses fractions None A collection of data objects that represent fractions of a single sample"},{"location":"ManifestCategoryEnum/#slots","title":"Slots","text":"Name Description manifest_category The type of context in which the constituent DataObjects can be analyzed toge..."},{"location":"ManifestCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ManifestCategoryEnum/#schema-source","title":"Schema Source","text":"name: ManifestCategoryEnum\ndescription: A list of contexts in which some DataObjects can be analyzed together.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n instrument_run:\n text: instrument_run\n description: A collection of data objects from a single run of an instrument.\n poolable_replicates:\n text: poolable_replicates\n description: A collection of data objects that can be pooled for downstream analyses.\n fractions:\n text: fractions\n description: A collection of data objects that represent fractions of a single\n sample.\n\nURI: MassAnalyzerEnum
"},{"location":"MassAnalyzerEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description time_of_flight None Instrument that separates ions by m/z in a field-free region after accelerati... quadrupole None A mass spectrometer that consists of four parallel rods whose centers form th... Orbitrap None An ion trapping device that consists of an outer barrel-like electrode and a ... ion_cyclotron_resonance None A mass spectrometer based on the principle of ion cyclotron resonance in whic... ion_trap None A device for spatially confining ions using electric and magnetic fields alon..."},{"location":"MassAnalyzerEnum/#slots","title":"Slots","text":"Name Description mass_analyzers The kind of mass analyzer(s) used during the spectra collection"},{"location":"MassAnalyzerEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassAnalyzerEnum/#schema-source","title":"Schema Source","text":"name: MassAnalyzerEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n time_of_flight:\n text: time_of_flight\n description: Instrument that separates ions by m/z in a field-free region after\n acceleration to a fixed acceleration energy.\n aliases:\n - TOF\n exact_mappings:\n - MS:1000084\n quadrupole:\n text: quadrupole\n description: A mass spectrometer that consists of four parallel rods whose centers\n form the corners of a square and whose opposing poles are connected. The voltage\n applied to the rods is a superposition of a static potential and a sinusoidal\n radio frequency potential. The motion of an ion in the x and y dimensions is\n described by the Matthieu equation whose solutions show that ions in a particular\n m/z range can be transmitted along the z axis.\n aliases:\n - Quad\n - Q\n exact_mappings:\n - MS:1000081\n Orbitrap:\n text: Orbitrap\n description: An ion trapping device that consists of an outer barrel-like electrode\n and a coaxial inner spindle-like electrode that form an electrostatic field\n with quadro-logarithmic potential distribution. The frequency of harmonic oscillations\n of the orbitally trapped ions along the axis of the electrostatic field is independent\n of the ion velocity and is inversely proportional to the square root of m/z\n so that the trap can be used as a mass analyzer.\n aliases:\n - Orbi\n exact_mappings:\n - MS:1000484\n ion_cyclotron_resonance:\n text: ion_cyclotron_resonance\n description: A mass spectrometer based on the principle of ion cyclotron resonance\n in which an ion in a magnetic field moves in a circular orbit at a frequency\n characteristic of its m/z value. Ions are coherently excited to a larger radius\n orbit using a pulse of radio frequency energy and their image charge is detected\n on receiver plates as a time domain signal. Fourier transformation of the time\n domain signal results in a frequency domain signal which is converted to a mass\n spectrum based in the inverse relationship between frequency and m/z.\n aliases:\n - ICR\n exact_mappings:\n - MS:1000079\n ion_trap:\n text: ion_trap\n description: A device for spatially confining ions using electric and magnetic\n fields alone or in combination.\n aliases:\n - LTQ\n - Ion Trap\n - Paul Trap\n exact_mappings:\n - MS:1000264\n\nSpectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.
URI: nmdc:MassSpectrometry
classDiagram\n class MassSpectrometry\n click MassSpectrometry href \"../MassSpectrometry\"\n DataGeneration <|-- MassSpectrometry\n click DataGeneration href \"../DataGeneration\"\n\n\n\n MassSpectrometry : add_date\n\n MassSpectrometry : alternative_identifiers\n\n MassSpectrometry : analyte_category\n\n MassSpectrometry --> \"1\" MassSpectrometryEnum : analyte_category\n click MassSpectrometryEnum href \"../MassSpectrometryEnum\"\n\n MassSpectrometry : associated_studies\n\n MassSpectrometry --> \"1..*\" Study : associated_studies\n click Study href \"../Study\"\n\n MassSpectrometry : description\n\n MassSpectrometry : eluent_introduction_category\n\n MassSpectrometry --> \"0..1\" EluentIntroductionCategoryEnum : eluent_introduction_category\n click EluentIntroductionCategoryEnum href \"../EluentIntroductionCategoryEnum\"\n\n MassSpectrometry : end_date\n\n MassSpectrometry : generates_calibration\n\n MassSpectrometry --> \"0..1\" CalibrationInformation : generates_calibration\n click CalibrationInformation href \"../CalibrationInformation\"\n\n MassSpectrometry : has_chromatography_configuration\n\n MassSpectrometry --> \"0..1\" ChromatographyConfiguration : has_chromatography_configuration\n click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n\n MassSpectrometry : has_failure_categorization\n\n MassSpectrometry --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MassSpectrometry : has_input\n\n MassSpectrometry --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n MassSpectrometry : has_mass_spectrometry_configuration\n\n MassSpectrometry --> \"0..1\" MassSpectrometryConfiguration : has_mass_spectrometry_configuration\n click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n\n MassSpectrometry : has_output\n\n MassSpectrometry --> \"*\" DataObject : has_output\n click DataObject href \"../DataObject\"\n\n MassSpectrometry : id\n\n MassSpectrometry : instrument_used\n\n MassSpectrometry --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n MassSpectrometry : mod_date\n\n MassSpectrometry : name\n\n MassSpectrometry : principal_investigator\n\n MassSpectrometry --> \"0..1\" PersonValue : principal_investigator\n click PersonValue href \"../PersonValue\"\n\n MassSpectrometry : processing_institution\n\n MassSpectrometry --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MassSpectrometry : protocol_link\n\n MassSpectrometry --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MassSpectrometry : qc_comment\n\n MassSpectrometry : qc_status\n\n MassSpectrometry --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MassSpectrometry : start_date\n\n MassSpectrometry : type\n\n\n\nname: MassSpectrometry\ndescription: Spectrometry where the sample is converted into gaseous ions which are\n characterised by their mass-to-charge ratio and relative abundance.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- CHMO:0000470\nis_a: DataGeneration\nslots:\n- eluent_introduction_category\n- generates_calibration\n- has_chromatography_configuration\n- has_mass_spectrometry_configuration\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_chromatography_configuration:\n name: has_chromatography_configuration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_mass_spectrometry_configuration:\n name: has_mass_spectrometry_configuration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\n analyte_category:\n name: analyte_category\n range: MassSpectrometryEnum\nclass_uri: nmdc:MassSpectrometry\nrules:\n- preconditions:\n slot_conditions:\n eluent_introduction_category:\n name: eluent_introduction_category\n equals_string: gas_chromatography\n postconditions:\n slot_conditions:\n generates_calibration:\n name: generates_calibration\n required: true\n description: If eluent_introduction_category is gas_chromatography, then generates_calibration\n is required.\n title: generates_calibration_required_if_gc\n- preconditions:\n slot_conditions:\n eluent_introduction_category:\n name: eluent_introduction_category\n any_of:\n - equals_string: liquid_chromatography\n - equals_string: gas_chromatography\n postconditions:\n slot_conditions:\n has_chromatography_configuration:\n name: has_chromatography_configuration\n required: true\n description: If eluent_introduction_category is liquid_chromatography or gas_chromatography,\n then has_chromatography_configuration is required.\n title: has_chromatography_configuration_required_if_lc_or_gc\n\nname: MassSpectrometry\ndescription: Spectrometry where the sample is converted into gaseous ions which are\n characterised by their mass-to-charge ratio and relative abundance.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- CHMO:0000470\nis_a: DataGeneration\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_chromatography_configuration:\n name: has_chromatography_configuration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_mass_spectrometry_configuration:\n name: has_mass_spectrometry_configuration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\n analyte_category:\n name: analyte_category\n range: MassSpectrometryEnum\nattributes:\n eluent_introduction_category:\n name: eluent_introduction_category\n description: A high-level categorization for how the processed sample is introduced\n into a mass spectrometer.\n examples:\n - value: liquid_chromatography\n - value: direct_infusion_syringe\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: eluent_introduction_category\n owner: MassSpectrometry\n domain_of:\n - MassSpectrometry\n range: EluentIntroductionCategoryEnum\n generates_calibration:\n name: generates_calibration\n description: calibration information is generated a process\n comments:\n - A gas chromatography mass spectromery run generates data to calibrate the retention\n index\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: generates_calibration\n owner: MassSpectrometry\n domain_of:\n - MassSpectrometry\n range: CalibrationInformation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_chromatography_configuration:\n name: has_chromatography_configuration\n description: The identifier of the associated ChromatographyConfiguration, providing\n information about how a sample was introduced into the mass spectrometer.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_chromatography_configuration\n owner: MassSpectrometry\n domain_of:\n - MassSpectrometry\n range: ChromatographyConfiguration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_mass_spectrometry_configuration:\n name: has_mass_spectrometry_configuration\n description: The identifier of the associated MassSpectrometryConfiguration.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_mass_spectrometry_configuration\n owner: MassSpectrometry\n domain_of:\n - MassSpectrometry\n range: MassSpectrometryConfiguration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: MassSpectrometry\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n analyte_category:\n name: analyte_category\n description: \"The type of analyte(s) that were measured in the data generation\\\n \\ process and analyzed\\n in the Workflow Chain\\n\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: analyte_category\n owner: MassSpectrometry\n domain_of:\n - DataGeneration\n range: MassSpectrometryEnum\n required: true\n associated_studies:\n name: associated_studies\n description: The study associated with a resource.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: associated_studies\n owner: MassSpectrometry\n domain_of:\n - Biosample\n - DataGeneration\n range: Study\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: MassSpectrometry\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: MassSpectrometry\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n alias: principal_investigator\n owner: MassSpectrometry\n domain_of:\n - Study\n - DataGeneration\n range: PersonValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: DataObject\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MassSpectrometry\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MassSpectrometry\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MassSpectrometry\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MassSpectrometry\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MassSpectrometry\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MassSpectrometry\nrules:\n- preconditions:\n slot_conditions:\n eluent_introduction_category:\n name: eluent_introduction_category\n equals_string: gas_chromatography\n postconditions:\n slot_conditions:\n generates_calibration:\n name: generates_calibration\n required: true\n description: If eluent_introduction_category is gas_chromatography, then generates_calibration\n is required.\n title: generates_calibration_required_if_gc\n- preconditions:\n slot_conditions:\n eluent_introduction_category:\n name: eluent_introduction_category\n any_of:\n - equals_string: liquid_chromatography\n - equals_string: gas_chromatography\n postconditions:\n slot_conditions:\n has_chromatography_configuration:\n name: has_chromatography_configuration\n required: true\n description: If eluent_introduction_category is liquid_chromatography or gas_chromatography,\n then has_chromatography_configuration is required.\n title: has_chromatography_configuration_required_if_lc_or_gc\n\nURI: MassSpectrometryAcquisitionStrategyEnum
"},{"location":"MassSpectrometryAcquisitionStrategyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description data_independent_acquisition None ['Data independent mass spectrometer acquisition method wherein the full mass... data_dependent_acquisition None Mass spectrometer data acquisition method wherein MSn spectra are triggered b... full_scan_only None Mass spectrometer data acquisition method wherein only MS1 data are acquired"},{"location":"MassSpectrometryAcquisitionStrategyEnum/#slots","title":"Slots","text":"Name Description mass_spectrometry_acquisition_strategy Mode of running a mass spectrometer method by which m/z ranges are selected a..."},{"location":"MassSpectrometryAcquisitionStrategyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometryAcquisitionStrategyEnum/#schema-source","title":"Schema Source","text":"name: MassSpectrometryAcquisitionStrategyEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n data_independent_acquisition:\n text: data_independent_acquisition\n description: '[''Data independent mass spectrometer acquisition method wherein\n the full mass range is fragmented. Examples of such an approach include MS^E,\n AIF, and bbCID.'']'\n aliases:\n - DIA\n - data independent acquisition from dissociation of full mass range\n exact_mappings:\n - MS:1003227\n data_dependent_acquisition:\n text: data_dependent_acquisition\n description: Mass spectrometer data acquisition method wherein MSn spectra are\n triggered based on the m/z of precursor ions detected in the same run.\n aliases:\n - -DDA\n exact_mappings:\n - MS:1003221\n full_scan_only:\n text: full_scan_only\n description: Mass spectrometer data acquisition method wherein only MS1 data are\n acquired.\n aliases:\n - MS\n\nA set of parameters that define and control the actions of a mass spectrometry process.
URI: nmdc:MassSpectrometryConfiguration
classDiagram\n class MassSpectrometryConfiguration\n click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n Configuration <|-- MassSpectrometryConfiguration\n click Configuration href \"../Configuration\"\n\n\n\n MassSpectrometryConfiguration : alternative_identifiers\n\n MassSpectrometryConfiguration : description\n\n MassSpectrometryConfiguration : id\n\n MassSpectrometryConfiguration : ionization_source\n\n MassSpectrometryConfiguration --> \"0..1\" IonizationSourceEnum : ionization_source\n click IonizationSourceEnum href \"../IonizationSourceEnum\"\n\n MassSpectrometryConfiguration : mass_analyzers\n\n MassSpectrometryConfiguration --> \"*\" MassAnalyzerEnum : mass_analyzers\n click MassAnalyzerEnum href \"../MassAnalyzerEnum\"\n\n MassSpectrometryConfiguration : mass_spectrometry_acquisition_strategy\n\n MassSpectrometryConfiguration --> \"0..1\" MassSpectrometryAcquisitionStrategyEnum : mass_spectrometry_acquisition_strategy\n click MassSpectrometryAcquisitionStrategyEnum href \"../MassSpectrometryAcquisitionStrategyEnum\"\n\n MassSpectrometryConfiguration : mass_spectrum_collection_modes\n\n MassSpectrometryConfiguration --> \"*\" MassSpectrumCollectionModeEnum : mass_spectrum_collection_modes\n click MassSpectrumCollectionModeEnum href \"../MassSpectrumCollectionModeEnum\"\n\n MassSpectrometryConfiguration : name\n\n MassSpectrometryConfiguration : polarity_mode\n\n MassSpectrometryConfiguration --> \"0..1\" PolarityModeEnum : polarity_mode\n click PolarityModeEnum href \"../PolarityModeEnum\"\n\n MassSpectrometryConfiguration : resolution_categories\n\n MassSpectrometryConfiguration --> \"*\" ResolutionCategoryEnum : resolution_categories\n click ResolutionCategoryEnum href \"../ResolutionCategoryEnum\"\n\n MassSpectrometryConfiguration : type\n\n\n\nname: MassSpectrometryConfiguration\ndescription: A set of parameters that define and control the actions of a mass spectrometry\n process.\nnotes:\n- This class is intended to represent a mass spectrometry method file that controls\n a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslots:\n- mass_spectrometry_acquisition_strategy\n- resolution_categories\n- mass_analyzers\n- ionization_source\n- mass_spectrum_collection_modes\n- polarity_mode\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MassSpectrometryConfiguration\n\nname: MassSpectrometryConfiguration\ndescription: A set of parameters that define and control the actions of a mass spectrometry\n process.\nnotes:\n- This class is intended to represent a mass spectrometry method file that controls\n a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n mass_spectrometry_acquisition_strategy:\n name: mass_spectrometry_acquisition_strategy\n description: Mode of running a mass spectrometer method by which m/z ranges are\n selected and ions possibly fragment.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - MS:1003213\n rank: 1000\n alias: mass_spectrometry_acquisition_strategy\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: MassSpectrometryAcquisitionStrategyEnum\n resolution_categories:\n name: resolution_categories\n description: The relative resolution at which spectra were collected.\n examples:\n - value: '[''high'', ''low'']'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: resolution_categories\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: ResolutionCategoryEnum\n multivalued: true\n mass_analyzers:\n name: mass_analyzers\n description: The kind of mass analyzer(s) used during the spectra collection.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - MS:1000443\n rank: 1000\n alias: mass_analyzers\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: MassAnalyzerEnum\n multivalued: true\n ionization_source:\n name: ionization_source\n description: The ionization source used to introduce processed samples into a\n mass spectrometer\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - MS:1000008\n rank: 1000\n alias: ionization_source\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: IonizationSourceEnum\n mass_spectrum_collection_modes:\n name: mass_spectrum_collection_modes\n description: Indicates whether mass spectra were collected in full profile, reduced\n profile, or centroid mode during acquisition.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mass_spectrum_collection_modes\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: MassSpectrumCollectionModeEnum\n multivalued: true\n polarity_mode:\n name: polarity_mode\n description: the polarity of which ions are generated and detected\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: polarity_mode\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: PolarityModeEnum\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MassSpectrometryConfiguration\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MassSpectrometryConfiguration\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n required: true\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MassSpectrometryConfiguration\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n required: true\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MassSpectrometryConfiguration\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MassSpectrometryConfiguration\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MassSpectrometryConfiguration\n\nURI: MassSpectrometryEnum
"},{"location":"MassSpectrometryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metaproteome None metabolome None lipidome None nom None"},{"location":"MassSpectrometryEnum/#slots","title":"Slots","text":"Name Description analyte_category"},{"location":"MassSpectrometryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometryEnum/#schema-source","title":"Schema Source","text":"name: MassSpectrometryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metaproteome:\n text: metaproteome\n title: Metaproteome\n aliases:\n - metaP\n metabolome:\n text: metabolome\n title: Metabolome\n aliases:\n - metaB\n lipidome:\n text: lipidome\n title: Lipidome\n nom:\n text: nom\n title: Natural Organic Matter\n aliases:\n - natural organic matter\n\nURI: MassSpectrumCollectionModeEnum
"},{"location":"MassSpectrumCollectionModeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description full_profile None reduced_profile None centroid None"},{"location":"MassSpectrumCollectionModeEnum/#slots","title":"Slots","text":"Name Description mass_spectrum_collection_modes Indicates whether mass spectra were collected in full profile, reduced profil..."},{"location":"MassSpectrumCollectionModeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrumCollectionModeEnum/#schema-source","title":"Schema Source","text":"name: MassSpectrumCollectionModeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n full_profile:\n text: full_profile\n reduced_profile:\n text: reduced_profile\n centroid:\n text: centroid\n\nNote
This is an abstract class and should not be instantiated directly.
URI: nmdc:MaterialEntity
classDiagram\n class MaterialEntity\n click MaterialEntity href \"../MaterialEntity\"\n NamedThing <|-- MaterialEntity\n click NamedThing href \"../NamedThing\"\n\n\n MaterialEntity <|-- Sample\n click Sample href \"../Sample\"\n MaterialEntity <|-- Site\n click Site href \"../Site\"\n MaterialEntity <|-- Instrument\n click Instrument href \"../Instrument\"\n\n\n\n MaterialEntity : alternative_identifiers\n\n MaterialEntity : description\n\n MaterialEntity : id\n\n MaterialEntity : name\n\n MaterialEntity : type\n\n\n\nname: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nclass_uri: nmdc:MaterialEntity\n\nname: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MaterialEntity\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MaterialEntity\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MaterialEntity\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MaterialEntity\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MaterialEntity\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MaterialEntity\n\nA process that takes one or more samples as inputs and generates one or more samples as outputs.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:MaterialProcessing
classDiagram\n class MaterialProcessing\n click MaterialProcessing href \"../MaterialProcessing\"\n PlannedProcess <|-- MaterialProcessing\n click PlannedProcess href \"../PlannedProcess\"\n\n\n MaterialProcessing <|-- Pooling\n click Pooling href \"../Pooling\"\n MaterialProcessing <|-- Extraction\n click Extraction href \"../Extraction\"\n MaterialProcessing <|-- LibraryPreparation\n click LibraryPreparation href \"../LibraryPreparation\"\n MaterialProcessing <|-- SubSamplingProcess\n click SubSamplingProcess href \"../SubSamplingProcess\"\n MaterialProcessing <|-- MixingProcess\n click MixingProcess href \"../MixingProcess\"\n MaterialProcessing <|-- FiltrationProcess\n click FiltrationProcess href \"../FiltrationProcess\"\n MaterialProcessing <|-- ChromatographicSeparationProcess\n click ChromatographicSeparationProcess href \"../ChromatographicSeparationProcess\"\n MaterialProcessing <|-- DissolvingProcess\n click DissolvingProcess href \"../DissolvingProcess\"\n MaterialProcessing <|-- ChemicalConversionProcess\n click ChemicalConversionProcess href \"../ChemicalConversionProcess\"\n\n\n\n MaterialProcessing : alternative_identifiers\n\n MaterialProcessing : description\n\n MaterialProcessing : end_date\n\n MaterialProcessing : has_failure_categorization\n\n MaterialProcessing --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MaterialProcessing : has_input\n\n MaterialProcessing --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n MaterialProcessing : has_output\n\n MaterialProcessing --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n MaterialProcessing : id\n\n MaterialProcessing : instrument_used\n\n MaterialProcessing --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n MaterialProcessing : name\n\n MaterialProcessing : processing_institution\n\n MaterialProcessing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MaterialProcessing : protocol_link\n\n MaterialProcessing --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MaterialProcessing : qc_comment\n\n MaterialProcessing : qc_status\n\n MaterialProcessing --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MaterialProcessing : start_date\n\n MaterialProcessing : type\n\n\n\nname: MaterialProcessing\ndescription: A process that takes one or more samples as inputs and generates one\n or more samples as outputs.\nnotes:\n- This class is a replacement for BiosampleProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nabstract: true\nslots:\n- instrument_used\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MaterialProcessing\n\nname: MaterialProcessing\ndescription: A process that takes one or more samples as inputs and generates one\n or more samples as outputs.\nnotes:\n- This class is a replacement for BiosampleProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: MaterialProcessing\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MaterialProcessing\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MaterialProcessing\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MaterialProcessing\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MaterialProcessing\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MaterialProcessing\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MaterialProcessing\n\nURI: MechStrucEnum
"},{"location":"MechStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description subway None coach None carriage None elevator None escalator None boat None train None car None bus None"},{"location":"MechStrucEnum/#slots","title":"Slots","text":"Name Description mech_struc mechanical structure: a moving structure"},{"location":"MechStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MechStrucEnum/#schema-source","title":"Schema Source","text":"name: mech_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n subway:\n text: subway\n coach:\n text: coach\n carriage:\n text: carriage\n elevator:\n text: elevator\n escalator:\n text: escalator\n boat:\n text: boat\n train:\n text: train\n car:\n text: car\n bus:\n text: bus\n\nThis is used to link a metabolomics analysis workflow to a specific metabolite
URI: nmdc:MetaboliteIdentification
classDiagram\n class MetaboliteIdentification\n click MetaboliteIdentification href \"../MetaboliteIdentification\"\n\n MetaboliteIdentification : alternative_identifiers\n\n MetaboliteIdentification : highest_similarity_score\n\n MetaboliteIdentification : metabolite_identified\n\n MetaboliteIdentification : type\n\n\n\nname: MetaboliteIdentification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- alternative_identifiers\n- highest_similarity_score\n- metabolite_identified\n- type\nclass_uri: nmdc:MetaboliteIdentification\n\nname: MetaboliteIdentification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetaboliteIdentification\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n highest_similarity_score:\n name: highest_similarity_score\n todos:\n - Yuri to fill in description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: highest_similarity_score\n owner: MetaboliteIdentification\n domain_of:\n - MetaboliteIdentification\n range: float\n metabolite_identified:\n name: metabolite_identified\n description: the specific metabolite identifier\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: metabolite_identified\n owner: MetaboliteIdentification\n domain_of:\n - MetaboliteIdentification\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetaboliteIdentification\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetaboliteIdentification\n\nURI: nmdc:MetabolomicsAnalysis
classDiagram\n class MetabolomicsAnalysis\n click MetabolomicsAnalysis href \"../MetabolomicsAnalysis\"\n WorkflowExecution <|-- MetabolomicsAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetabolomicsAnalysis : alternative_identifiers\n\n MetabolomicsAnalysis : description\n\n MetabolomicsAnalysis : end_date\n\n MetabolomicsAnalysis : ended_at_time\n\n MetabolomicsAnalysis : execution_resource\n\n MetabolomicsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetabolomicsAnalysis : git_url\n\n MetabolomicsAnalysis : has_failure_categorization\n\n MetabolomicsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetabolomicsAnalysis : has_input\n\n MetabolomicsAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetabolomicsAnalysis : has_metabolite_identifications\n\n MetabolomicsAnalysis --> \"*\" MetaboliteIdentification : has_metabolite_identifications\n click MetaboliteIdentification href \"../MetaboliteIdentification\"\n\n MetabolomicsAnalysis : has_output\n\n MetabolomicsAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetabolomicsAnalysis : id\n\n MetabolomicsAnalysis : name\n\n MetabolomicsAnalysis : processing_institution\n\n MetabolomicsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetabolomicsAnalysis : protocol_link\n\n MetabolomicsAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetabolomicsAnalysis : qc_comment\n\n MetabolomicsAnalysis : qc_status\n\n MetabolomicsAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetabolomicsAnalysis : start_date\n\n MetabolomicsAnalysis : started_at_time\n\n MetabolomicsAnalysis : type\n\n MetabolomicsAnalysis : uses_calibration\n\n MetabolomicsAnalysis --> \"0..1\" CalibrationInformation : uses_calibration\n click CalibrationInformation href \"../CalibrationInformation\"\n\n MetabolomicsAnalysis : version\n\n MetabolomicsAnalysis : was_informed_by\n\n MetabolomicsAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetabolomicsAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- has_metabolite_identifications\n- uses_calibration\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetabolomicsAnalysis\n\nname: MetabolomicsAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n has_metabolite_identifications:\n name: has_metabolite_identifications\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_metabolite_identifications\n owner: MetabolomicsAnalysis\n domain_of:\n - MetabolomicsAnalysis\n range: MetaboliteIdentification\n multivalued: true\n inlined: true\n inlined_as_list: true\n uses_calibration:\n name: uses_calibration\n description: calibration information is used by a process\n comments:\n - Retenion index calibration data generated by a gas chromatography mass spectromery\n run is used when analyzing metabolomics data\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: uses_calibration\n owner: MetabolomicsAnalysis\n domain_of:\n - MetabolomicsAnalysis\n - NomAnalysis\n range: CalibrationInformation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetabolomicsAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetabolomicsAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetabolomicsAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetabolomicsAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetabolomicsAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetabolomicsAnalysis\n\nThis documentation provides details on the National Microbiome Data Collaborative\u2019s (NMDC) approach to sample and data processing metadata. These are key features that drive the data search and discovery aspect of the NMDC data portal (https://microbiomedata.org/data/). If you are unfamiliar with these types of metadata (Figure 1), we recommend you begin with an Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask) (https://doi.org/10.25979/1607365).
Figure 1: Microbiome metadata types: Information that contextualizes sample including its geographic location and collection date, sample preparation, data processing methods, and data products produced from a biological sample (Luke et al., 2020. Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask). DOI: 10.25979/1607365).
All data integrated into the NMDC data portal must adhere to existing metadata standards for proper indexing and display, and to ensure accurate search results are returned. This documentation outlines the standards and ontologies that were included in the NMDC data schema, a framework that defines how data were defined and linked. For the 2019-2022 pilot initiative, the NMDC Metadata Standards Team (see the NMDC Team page) leveraged existing community-driven standards developed by the Genomics Standards Consortium (GSC), the Joint Genome Institute (JGI) Genomes Online Database (GOLD), and OBO Foundry\u2019s Environmental Ontology (EnvO). In collaboration with these organizations, the NMDC has created a framework for mapping these standards into an interoperable framework that can be expanded to include additional standards and ontologies in the future.
Additional information on the activities by the NMDC Metadata Standards team can be found on the NMDC website at: https://microbiomedata.org/metadata/
"},{"location":"Metadata_Documentation_Overview/#standards-and-ontologies-used-by-the-nmdc","title":"Standards and Ontologies used by the NMDC","text":""},{"location":"Metadata_Documentation_Overview/#sample-metadata","title":"Sample Metadata","text":""},{"location":"Metadata_Documentation_Overview/#gsc-minimum-information-about-any-x-sequence-mixs","title":"GSC Minimum Information about any (x) Sequence (MIxS)","text":"The GSC has developed standards for describing genomic and metagenomic sequences, including the \u201cminimum information about a genome sequence\u201d (MIGS), the \u201cminimum information about a metagenome sequence\u201d (MIMS), and the \u201cminimum information about a marker gene sequence\u201d (MIMARKS). To complement this community-driven standard effort, the GSC has also developed a system for describing the environment from which a biological sample originates, as \u201cenvironmental packages\u201d and established a unified standard set of checklists through the minimum information about any (x) sequence (MIxS). MIxS provides a standardized data dictionary of sample descriptors (e.g., location, environment, elevation, altitude, depth, etc.) organized into different packages for 17 different sample environments.
To standardize how physical samples are described (i.e., sample metadata, Figure 1), the NMDC Schema includes environmental descriptors from the GSC MIxS standards.
Explore how to create a MIxS-compliant sample metadata spreadsheet
Review our example spreadsheet with sample metadata that has been converted to be compliant with the MIxS Soil environment package. Note that not all non-mandatory terms from the MIxs Soil package were relevant for these example samples, and hence were omitted for clarity.
Basic sample spreadsheet (Tab 1 - before conversion to MIxS)
MIxS-compliant soil spreadsheet (Tab 2 - converted to MIxS Soil)
Explore the mandatory, unique, and shared descriptors from the MIxS Soil package
Searchable descriptors from all MIxS environmental packages - coming soon!
Learn more about all of the 17 MIxS environmental packages
The JGI Genomes OnLine Database (GOLD, Mukherjee 2021) is an open-access repository of genome, metagenome, and metatranscriptome sequencing projects with their associated metadata. GOLD data are organized based on Study, Biosample/Organism, Sequencing Project and Analysis Project (Mukherjee 2017). Biosamples (defined as the physical material collected from an environment) are described using a five-level ecosystem classification path (Figure 2); the NMDC schema also uses this ecosystem classification to describe sample environments.
Figure 2. The GOLD five-level ecosystem classification paths (Mukherjee 2019).
Overview of the GOLD ecosystem paths
Ecosystem describes biosamples using three different broadest contexts, namely environmental, engineered, and host-associated.
Ecosystem category subdivides the ecosystem into categories, such as aquatic or terrestrial.
Ecosystem type classifies those categories into types, such as freshwater or marine, cave, desert, soil, etc.
Ecosystem subtype allows for additional environmental context or boundaries.
Specific ecosystem that describes the environment that directly influences the sample or the environmental material itself.
Explore how to map sample environments using the GOLD ecosystem classification
Learn more about the GOLD ecosystem paths using an interactive visualization tool.
Review a step-by-step example of how to assign the GOLD ecosystem classification to a lake sediment sample.
The Environment Ontology (EnvO, Buttigieg 2016) is a community-led ontology that represents environmental entities such as biomes, environmental features, and environmental materials. Each EnvO term is identified using a unique resource identifier (e.g., CURIE or IRI) that resolves in a web browser. This ensures that EnvO\u2019s terms (and their definitions) are easy to find, reference, and share amongst collaborators. It also ensures that datasets described using EnvO terms can be more easily integrated and analyzed in a reproducible manner. And since the meanings of the terms are precisely defined and accessible, humans and computers can easily connect EnvO terms across datasets.
EnvO terms are the recommended values for several of the mandatory terms in the MIxS packages, often referred to as the \"MIxS triad\u201d.
MIxS: env_broad_scale (a.k.a. Biome): The major environmental system that the sample or specimen came from. Often, the value for this term comes from EnvO\u2019s biome hierarchy, and is similar to GOLD\u2019s Ecosystem category.
MIxS: env_local_scale (a.k.a. Feature): A more direct expression of the sample or specimen\u2019s local vicinity, which likely has a significant influence on the sample or specimen. Possible values are listed in EnvO\u2019s astronomical body part hierarchy, which is similar to GOLD\u2019s Ecosystem type/subtype.
MIxS: env_medium (a.k.a. material): The environmental material(s) immediately surrounding your sample or specimen prior to sampling. Examples of this are found in EnvO\u2019s environmental material hierarchy, and is similar to GOLD\u2019s Specific ecosystem.
Explore how to map sample environments using the EnvO ecosystem classification
Review a step-by-step example of how to assign EnvO terms to an oligotrophic lake sediment sample below.
env_broad_scale (Biome)
Using EnvO biome categories, aquatic is appropriate. However, since the EnvO is a hierarchical system, the aquatic biome has two sub-categories: freshwater and marine biomes. The freshwater biome is further divided into freshwater lake biome and freshwater river biome. Therefore, for a lake sediment sample, freshwater lake biome is the appropriate EnvO biome category.
env_local_scale (Feature)
Next, we describe the local environmental feature in the vicinity of and likely having a strong causal influence on the sample. Using the EnvO astronomical body part categories, we step through the relevant categories (see figure on the right) until we reach the EnvO term oligotrophic lake.
env_medium (Material)
Finally, since the sample is oligotrophic lake sediment, the EnvO environmental material could be assigned sediment. But because the EnvO hierarchy provides sub-categories within sediment, the environmenta material will be assigned lake sediment.
Therefore, the EnvO triad for oligotrophic lake sediment is:
Env_broad_scale: freshwater lake biome [ENVO_01000252]
Env_local_scale: oligotrophic lake [ENVO_01000774]
Env_medium: lake sediment [ENVO_00000546]
"},{"location":"Metadata_Documentation_Overview/#classifying-samples-with-gold-and-mixsenvo","title":"Classifying samples with GOLD and MIxS/EnvO","text":"The five-level GOLD ecosystem classification path and EnvO triad each have unique advantages in describing the environmental context of a biosample. The NMDC leverages the strengths of both the GOLD ecosystem classification path and MIxS/EnvO triad. The assignment of MIxS/EnvO triad for the biosamples currently in the NMDC data portal was achieved through a manual curation process using various metadata fields of GOLD biosamples fields, such as name, description, habitat, sample collection site, identifier, ecosystem classification path, and study description. The NMDC team is currently working on exploring solutions for automated mapping between GOLD and MIxS/EnvO.
Figure 3: Mapping between the MIxS/EnvO triad and the GOLD ecosystem classification enables integration of sample environments defined with GOLD and MIxS/EnvO.
"},{"location":"Metadata_Documentation_Overview/#data-processing-metadata","title":"Data Processing Metadata","text":"In addition, the NMDC is adopting the MIxS standards for sequence data types (e.g., sequencing method, pcr primers and conditions, etc.), and are building on previous efforts by the Proteomics Standards Initiative and Metabolomics Standards Initiative to develop standards and controlled vocabularies for mass spectrometry data types (e.g., ionization mode, mass resolution, scan rate, etc.). Additional details on the processing metadata are coming soon.
"},{"location":"Metadata_Documentation_Overview/#overview-of-the-nmdc-data-schema","title":"Overview of the NMDC Data Schema","text":"The NMDC has developed a normalized metadata schema (available in the NMDC GitHub) for representing studies, samples, relationships between samples, and associated data objects. The schema is organized into object classes, which act as nodes. Each class has associated slots, which are fields that contain metadata that describe the object. For more in-depth information, full documentation of the NMDC Schema can be found here.
For the NMDC pilot, a python toolkit for generating NMDC-compliant JavaScript Object Notation (JSON) objects was developed to create ETL (Extract-Transform-Load) software to ingest metadata from the DOE User Facilities. Read more about the data in the NMDC pilot here.
"},{"location":"MetagenomeAnnotation/","title":"Class: MetagenomeAnnotation","text":"A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs
URI: nmdc:MetagenomeAnnotation
classDiagram\n class MetagenomeAnnotation\n click MetagenomeAnnotation href \"../MetagenomeAnnotation\"\n WorkflowExecution <|-- MetagenomeAnnotation\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetagenomeAnnotation : alternative_identifiers\n\n MetagenomeAnnotation : description\n\n MetagenomeAnnotation : end_date\n\n MetagenomeAnnotation : ended_at_time\n\n MetagenomeAnnotation : execution_resource\n\n MetagenomeAnnotation --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetagenomeAnnotation : git_url\n\n MetagenomeAnnotation : gold_analysis_project_identifiers\n\n MetagenomeAnnotation : has_failure_categorization\n\n MetagenomeAnnotation --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetagenomeAnnotation : has_input\n\n MetagenomeAnnotation --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetagenomeAnnotation : has_output\n\n MetagenomeAnnotation --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetagenomeAnnotation : id\n\n MetagenomeAnnotation : img_identifiers\n\n MetagenomeAnnotation : name\n\n MetagenomeAnnotation : processing_institution\n\n MetagenomeAnnotation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetagenomeAnnotation : protocol_link\n\n MetagenomeAnnotation --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetagenomeAnnotation : qc_comment\n\n MetagenomeAnnotation : qc_status\n\n MetagenomeAnnotation --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetagenomeAnnotation : start_date\n\n MetagenomeAnnotation : started_at_time\n\n MetagenomeAnnotation : type\n\n MetagenomeAnnotation : version\n\n MetagenomeAnnotation : was_informed_by\n\n MetagenomeAnnotation --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetagenomeAnnotation\ndescription: A workflow execution activity that provides functional and structural\n annotation of assembled metagenome contigs\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\n- gold_analysis_project_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\nclass_uri: nmdc:MetagenomeAnnotation\n\nname: MetagenomeAnnotation\ndescription: A workflow execution activity that provides functional and structural\n annotation of assembled metagenome contigs\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\nattributes:\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: MetagenomeAnnotation\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n maximum_cardinality: 1\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n description: identifiers for corresponding analysis projects in GOLD\n examples:\n - value: https://bioregistry.io/gold:Ga0526289\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: analysis_identifiers\n mixins:\n - gold_identifiers\n alias: gold_analysis_project_identifiers\n owner: MetagenomeAnnotation\n domain_of:\n - MetagenomeAnnotation\n - MetatranscriptomeAnnotation\n range: external_identifier\n multivalued: true\n pattern: ^gold:Ga[0-9]+$\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeAnnotation\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeAnnotation\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetagenomeAnnotation\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetagenomeAnnotation\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetagenomeAnnotation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetagenomeAnnotation\n\nA workflow execution activity that converts sequencing reads into an assembled metagenome.
URI: nmdc:MetagenomeAssembly
classDiagram\n class MetagenomeAssembly\n click MetagenomeAssembly href \"../MetagenomeAssembly\"\n WorkflowExecution <|-- MetagenomeAssembly\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetagenomeAssembly : alternative_identifiers\n\n MetagenomeAssembly : asm_score\n\n MetagenomeAssembly : contig_bp\n\n MetagenomeAssembly : contigs\n\n MetagenomeAssembly : ctg_l50\n\n MetagenomeAssembly : ctg_l90\n\n MetagenomeAssembly : ctg_logsum\n\n MetagenomeAssembly : ctg_max\n\n MetagenomeAssembly : ctg_n50\n\n MetagenomeAssembly : ctg_n90\n\n MetagenomeAssembly : ctg_powsum\n\n MetagenomeAssembly : description\n\n MetagenomeAssembly : end_date\n\n MetagenomeAssembly : ended_at_time\n\n MetagenomeAssembly : execution_resource\n\n MetagenomeAssembly --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetagenomeAssembly : gap_pct\n\n MetagenomeAssembly : gc_avg\n\n MetagenomeAssembly : gc_std\n\n MetagenomeAssembly : git_url\n\n MetagenomeAssembly : has_failure_categorization\n\n MetagenomeAssembly --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetagenomeAssembly : has_input\n\n MetagenomeAssembly --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetagenomeAssembly : has_output\n\n MetagenomeAssembly --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetagenomeAssembly : id\n\n MetagenomeAssembly : insdc_assembly_identifiers\n\n MetagenomeAssembly : name\n\n MetagenomeAssembly : num_aligned_reads\n\n MetagenomeAssembly : num_input_reads\n\n MetagenomeAssembly : processing_institution\n\n MetagenomeAssembly --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetagenomeAssembly : protocol_link\n\n MetagenomeAssembly --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetagenomeAssembly : qc_comment\n\n MetagenomeAssembly : qc_status\n\n MetagenomeAssembly --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetagenomeAssembly : scaf_bp\n\n MetagenomeAssembly : scaf_l50\n\n MetagenomeAssembly : scaf_l90\n\n MetagenomeAssembly : scaf_l_gt50k\n\n MetagenomeAssembly : scaf_logsum\n\n MetagenomeAssembly : scaf_max\n\n MetagenomeAssembly : scaf_n50\n\n MetagenomeAssembly : scaf_n90\n\n MetagenomeAssembly : scaf_n_gt50k\n\n MetagenomeAssembly : scaf_pct_gt50k\n\n MetagenomeAssembly : scaf_powsum\n\n MetagenomeAssembly : scaffolds\n\n MetagenomeAssembly : start_date\n\n MetagenomeAssembly : started_at_time\n\n MetagenomeAssembly : type\n\n MetagenomeAssembly : version\n\n MetagenomeAssembly : was_informed_by\n\n MetagenomeAssembly --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n relevant to NMDC\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetagenomeAssembly\n\nname: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n relevant to NMDC\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n asm_score:\n name: asm_score\n description: A score for comparing metagenomic assembly quality from same sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: asm_score\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaffolds:\n name: scaffolds\n description: Total sequence count of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaffolds\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_logsum:\n name: scaf_logsum\n description: The sum of the (length*log(length)) of all scaffolds, times some\n constant. Increase the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_logsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_powsum:\n name: scaf_powsum\n description: Powersum of all scaffolds is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_powsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_max:\n name: scaf_max\n description: Maximum scaffold length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_max\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_bp:\n name: scaf_bp\n description: Total size in bp of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_bp\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n50:\n name: scaf_n50\n description: Given a set of scaffolds, each with its own length, the N50 count\n is defined as the smallest number of scaffolds whose length sum makes up half\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n90:\n name: scaf_n90\n description: Given a set of scaffolds, each with its own length, the N90 count\n is defined as the smallest number of scaffolds whose length sum makes up 90%\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l50:\n name: scaf_l50\n description: Given a set of scaffolds, the L50 is defined as the sequence length\n of the shortest scaffold at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l90:\n name: scaf_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all scaffolds of that length or longer\n contains at least 90% of the sum of the lengths of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n_gt50k:\n name: scaf_n_gt50k\n description: Total sequence count of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l_gt50k:\n name: scaf_l_gt50k\n description: Total size in bp of all scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_pct_gt50k:\n name: scaf_pct_gt50k\n description: Total sequence size percentage of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_pct_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contigs:\n name: contigs\n description: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contigs\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contig_bp:\n name: contig_bp\n description: Total size in bp of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contig_bp\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n50:\n name: ctg_n50\n description: Given a set of contigs, each with its own length, the N50 count is\n defined as the smallest number_of_contigs whose length sum makes up half of\n genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l50:\n name: ctg_l50\n description: Given a set of contigs, the L50 is defined as the sequence length\n of the shortest contig at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n90:\n name: ctg_n90\n description: Given a set of contigs, each with its own length, the N90 count is\n defined as the smallest number of contigs whose length sum makes up 90% of genome\n size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l90:\n name: ctg_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all contigs of that length or longer\n contains at least 90% of the sum of the lengths of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_logsum:\n name: ctg_logsum\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_logsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_powsum:\n name: ctg_powsum\n description: Powersum of all contigs is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_powsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_max:\n name: ctg_max\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_max\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gap_pct:\n name: gap_pct\n description: The gap size percentage of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gap_pct\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_std:\n name: gc_std\n description: Standard deviation of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_std\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_avg:\n name: gc_avg\n description: Average of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_avg\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_input_reads:\n name: num_input_reads\n description: The sequence count number of input reads for assembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_input_reads\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_aligned_reads:\n name: num_aligned_reads\n description: The sequence count number of input reads aligned to assembled contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_aligned_reads\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n insdc_assembly_identifiers:\n name: insdc_assembly_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: assembly_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_assembly_identifiers\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: string\n pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeAssembly\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeAssembly\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetagenomeAssembly\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetagenomeAssembly\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetagenomeAssembly\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetagenomeAssembly\n\nInitial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.
URI: nmdc:MetagenomeSequencing
classDiagram\n class MetagenomeSequencing\n click MetagenomeSequencing href \"../MetagenomeSequencing\"\n WorkflowExecution <|-- MetagenomeSequencing\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetagenomeSequencing : alternative_identifiers\n\n MetagenomeSequencing : description\n\n MetagenomeSequencing : end_date\n\n MetagenomeSequencing : ended_at_time\n\n MetagenomeSequencing : execution_resource\n\n MetagenomeSequencing --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetagenomeSequencing : git_url\n\n MetagenomeSequencing : has_failure_categorization\n\n MetagenomeSequencing --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetagenomeSequencing : has_input\n\n MetagenomeSequencing --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetagenomeSequencing : has_output\n\n MetagenomeSequencing --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetagenomeSequencing : id\n\n MetagenomeSequencing : name\n\n MetagenomeSequencing : processing_institution\n\n MetagenomeSequencing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetagenomeSequencing : protocol_link\n\n MetagenomeSequencing --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetagenomeSequencing : qc_comment\n\n MetagenomeSequencing : qc_status\n\n MetagenomeSequencing --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetagenomeSequencing : start_date\n\n MetagenomeSequencing : started_at_time\n\n MetagenomeSequencing : type\n\n MetagenomeSequencing : version\n\n MetagenomeSequencing : was_informed_by\n\n MetagenomeSequencing --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetagenomeSequencing\ndescription: Initial sequencing activity that precedes any analysis. This activity\n has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetagenomeSequencing\n\nname: MetagenomeSequencing\ndescription: Initial sequencing activity that precedes any analysis. This activity\n has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeSequencing\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeSequencing\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetagenomeSequencing\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetagenomeSequencing\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetagenomeSequencing\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetagenomeSequencing\n\nURI: nmdc:MetaproteomicsAnalysis
classDiagram\n class MetaproteomicsAnalysis\n click MetaproteomicsAnalysis href \"../MetaproteomicsAnalysis\"\n WorkflowExecution <|-- MetaproteomicsAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetaproteomicsAnalysis : alternative_identifiers\n\n MetaproteomicsAnalysis : description\n\n MetaproteomicsAnalysis : end_date\n\n MetaproteomicsAnalysis : ended_at_time\n\n MetaproteomicsAnalysis : execution_resource\n\n MetaproteomicsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetaproteomicsAnalysis : git_url\n\n MetaproteomicsAnalysis : has_failure_categorization\n\n MetaproteomicsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetaproteomicsAnalysis : has_input\n\n MetaproteomicsAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetaproteomicsAnalysis : has_output\n\n MetaproteomicsAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetaproteomicsAnalysis : id\n\n MetaproteomicsAnalysis : metaproteomics_analysis_category\n\n MetaproteomicsAnalysis --> \"1\" MetaproteomicsAnalysisCategoryEnum : metaproteomics_analysis_category\n click MetaproteomicsAnalysisCategoryEnum href \"../MetaproteomicsAnalysisCategoryEnum\"\n\n MetaproteomicsAnalysis : name\n\n MetaproteomicsAnalysis : processing_institution\n\n MetaproteomicsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetaproteomicsAnalysis : protocol_link\n\n MetaproteomicsAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetaproteomicsAnalysis : qc_comment\n\n MetaproteomicsAnalysis : qc_status\n\n MetaproteomicsAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetaproteomicsAnalysis : start_date\n\n MetaproteomicsAnalysis : started_at_time\n\n MetaproteomicsAnalysis : type\n\n MetaproteomicsAnalysis : version\n\n MetaproteomicsAnalysis : was_informed_by\n\n MetaproteomicsAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetaproteomicsAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- metaproteomics_analysis_category\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetaproteomicsAnalysis\n\nname: MetaproteomicsAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n metaproteomics_analysis_category:\n name: metaproteomics_analysis_category\n description: The category of metaproteomics analysis being performed.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: metaproteomics_analysis_category\n owner: MetaproteomicsAnalysis\n domain_of:\n - MetaproteomicsAnalysis\n range: MetaproteomicsAnalysisCategoryEnum\n required: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetaproteomicsAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetaproteomicsAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetaproteomicsAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetaproteomicsAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetaproteomicsAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetaproteomicsAnalysis\n\nThe category of metaproteomics analysis being performed.
URI: MetaproteomicsAnalysisCategoryEnum
"},{"location":"MetaproteomicsAnalysisCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description matched_metagenome None A metaproteomics analysis that is matched to a metagenome derived from the sa... in_silico_metagenome None A metaproteomics analysis that is matched to an in silico generated metagenom..."},{"location":"MetaproteomicsAnalysisCategoryEnum/#slots","title":"Slots","text":"Name Description metaproteomics_analysis_category The category of metaproteomics analysis being performed"},{"location":"MetaproteomicsAnalysisCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetaproteomicsAnalysisCategoryEnum/#schema-source","title":"Schema Source","text":"name: MetaproteomicsAnalysisCategoryEnum\ndescription: The category of metaproteomics analysis being performed.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n matched_metagenome:\n text: matched_metagenome\n description: A metaproteomics analysis that is matched to a metagenome derived\n from the same biosample.\n in_silico_metagenome:\n text: in_silico_metagenome\n description: A metaproteomics analysis that is matched to an in silico generated\n metagenome.\n\nURI: nmdc:MetatranscriptomeAnnotation
classDiagram\n class MetatranscriptomeAnnotation\n click MetatranscriptomeAnnotation href \"../MetatranscriptomeAnnotation\"\n WorkflowExecution <|-- MetatranscriptomeAnnotation\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetatranscriptomeAnnotation : alternative_identifiers\n\n MetatranscriptomeAnnotation : description\n\n MetatranscriptomeAnnotation : end_date\n\n MetatranscriptomeAnnotation : ended_at_time\n\n MetatranscriptomeAnnotation : execution_resource\n\n MetatranscriptomeAnnotation --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetatranscriptomeAnnotation : git_url\n\n MetatranscriptomeAnnotation : gold_analysis_project_identifiers\n\n MetatranscriptomeAnnotation : has_failure_categorization\n\n MetatranscriptomeAnnotation --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetatranscriptomeAnnotation : has_input\n\n MetatranscriptomeAnnotation --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeAnnotation : has_output\n\n MetatranscriptomeAnnotation --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeAnnotation : id\n\n MetatranscriptomeAnnotation : img_identifiers\n\n MetatranscriptomeAnnotation : name\n\n MetatranscriptomeAnnotation : processing_institution\n\n MetatranscriptomeAnnotation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetatranscriptomeAnnotation : protocol_link\n\n MetatranscriptomeAnnotation --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetatranscriptomeAnnotation : qc_comment\n\n MetatranscriptomeAnnotation : qc_status\n\n MetatranscriptomeAnnotation --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetatranscriptomeAnnotation : start_date\n\n MetatranscriptomeAnnotation : started_at_time\n\n MetatranscriptomeAnnotation : type\n\n MetatranscriptomeAnnotation : version\n\n MetatranscriptomeAnnotation : was_informed_by\n\n MetatranscriptomeAnnotation --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetatranscriptomeAnnotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\n- gold_analysis_project_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\nclass_uri: nmdc:MetatranscriptomeAnnotation\n\nname: MetatranscriptomeAnnotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\nattributes:\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: MetatranscriptomeAnnotation\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n maximum_cardinality: 1\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n description: identifiers for corresponding analysis projects in GOLD\n examples:\n - value: https://bioregistry.io/gold:Ga0526289\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: analysis_identifiers\n mixins:\n - gold_identifiers\n alias: gold_analysis_project_identifiers\n owner: MetatranscriptomeAnnotation\n domain_of:\n - MetagenomeAnnotation\n - MetatranscriptomeAnnotation\n range: external_identifier\n multivalued: true\n pattern: ^gold:Ga[0-9]+$\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeAnnotation\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetatranscriptomeAnnotation\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetatranscriptomeAnnotation\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetatranscriptomeAnnotation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetatranscriptomeAnnotation\n\nURI: nmdc:MetatranscriptomeAssembly
classDiagram\n class MetatranscriptomeAssembly\n click MetatranscriptomeAssembly href \"../MetatranscriptomeAssembly\"\n WorkflowExecution <|-- MetatranscriptomeAssembly\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetatranscriptomeAssembly : alternative_identifiers\n\n MetatranscriptomeAssembly : asm_score\n\n MetatranscriptomeAssembly : contig_bp\n\n MetatranscriptomeAssembly : contigs\n\n MetatranscriptomeAssembly : ctg_l50\n\n MetatranscriptomeAssembly : ctg_l90\n\n MetatranscriptomeAssembly : ctg_logsum\n\n MetatranscriptomeAssembly : ctg_max\n\n MetatranscriptomeAssembly : ctg_n50\n\n MetatranscriptomeAssembly : ctg_n90\n\n MetatranscriptomeAssembly : ctg_powsum\n\n MetatranscriptomeAssembly : description\n\n MetatranscriptomeAssembly : end_date\n\n MetatranscriptomeAssembly : ended_at_time\n\n MetatranscriptomeAssembly : execution_resource\n\n MetatranscriptomeAssembly --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetatranscriptomeAssembly : gap_pct\n\n MetatranscriptomeAssembly : gc_avg\n\n MetatranscriptomeAssembly : gc_std\n\n MetatranscriptomeAssembly : git_url\n\n MetatranscriptomeAssembly : has_failure_categorization\n\n MetatranscriptomeAssembly --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetatranscriptomeAssembly : has_input\n\n MetatranscriptomeAssembly --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeAssembly : has_output\n\n MetatranscriptomeAssembly --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeAssembly : id\n\n MetatranscriptomeAssembly : insdc_assembly_identifiers\n\n MetatranscriptomeAssembly : name\n\n MetatranscriptomeAssembly : num_aligned_reads\n\n MetatranscriptomeAssembly : num_input_reads\n\n MetatranscriptomeAssembly : processing_institution\n\n MetatranscriptomeAssembly --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetatranscriptomeAssembly : protocol_link\n\n MetatranscriptomeAssembly --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetatranscriptomeAssembly : qc_comment\n\n MetatranscriptomeAssembly : qc_status\n\n MetatranscriptomeAssembly --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetatranscriptomeAssembly : scaf_bp\n\n MetatranscriptomeAssembly : scaf_l50\n\n MetatranscriptomeAssembly : scaf_l90\n\n MetatranscriptomeAssembly : scaf_l_gt50k\n\n MetatranscriptomeAssembly : scaf_logsum\n\n MetatranscriptomeAssembly : scaf_max\n\n MetatranscriptomeAssembly : scaf_n50\n\n MetatranscriptomeAssembly : scaf_n90\n\n MetatranscriptomeAssembly : scaf_n_gt50k\n\n MetatranscriptomeAssembly : scaf_pct_gt50k\n\n MetatranscriptomeAssembly : scaf_powsum\n\n MetatranscriptomeAssembly : scaffolds\n\n MetatranscriptomeAssembly : start_date\n\n MetatranscriptomeAssembly : started_at_time\n\n MetatranscriptomeAssembly : type\n\n MetatranscriptomeAssembly : version\n\n MetatranscriptomeAssembly : was_informed_by\n\n MetatranscriptomeAssembly --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetatranscriptomeAssembly\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetatranscriptomeAssembly\n\nname: MetatranscriptomeAssembly\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n asm_score:\n name: asm_score\n description: A score for comparing metagenomic assembly quality from same sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: asm_score\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaffolds:\n name: scaffolds\n description: Total sequence count of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaffolds\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_logsum:\n name: scaf_logsum\n description: The sum of the (length*log(length)) of all scaffolds, times some\n constant. Increase the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_logsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_powsum:\n name: scaf_powsum\n description: Powersum of all scaffolds is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_powsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_max:\n name: scaf_max\n description: Maximum scaffold length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_max\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_bp:\n name: scaf_bp\n description: Total size in bp of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_bp\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n50:\n name: scaf_n50\n description: Given a set of scaffolds, each with its own length, the N50 count\n is defined as the smallest number of scaffolds whose length sum makes up half\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n90:\n name: scaf_n90\n description: Given a set of scaffolds, each with its own length, the N90 count\n is defined as the smallest number of scaffolds whose length sum makes up 90%\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l50:\n name: scaf_l50\n description: Given a set of scaffolds, the L50 is defined as the sequence length\n of the shortest scaffold at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l90:\n name: scaf_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all scaffolds of that length or longer\n contains at least 90% of the sum of the lengths of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n_gt50k:\n name: scaf_n_gt50k\n description: Total sequence count of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l_gt50k:\n name: scaf_l_gt50k\n description: Total size in bp of all scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_pct_gt50k:\n name: scaf_pct_gt50k\n description: Total sequence size percentage of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_pct_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contigs:\n name: contigs\n description: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contigs\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contig_bp:\n name: contig_bp\n description: Total size in bp of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contig_bp\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n50:\n name: ctg_n50\n description: Given a set of contigs, each with its own length, the N50 count is\n defined as the smallest number_of_contigs whose length sum makes up half of\n genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l50:\n name: ctg_l50\n description: Given a set of contigs, the L50 is defined as the sequence length\n of the shortest contig at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n90:\n name: ctg_n90\n description: Given a set of contigs, each with its own length, the N90 count is\n defined as the smallest number of contigs whose length sum makes up 90% of genome\n size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l90:\n name: ctg_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all contigs of that length or longer\n contains at least 90% of the sum of the lengths of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_logsum:\n name: ctg_logsum\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_logsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_powsum:\n name: ctg_powsum\n description: Powersum of all contigs is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_powsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_max:\n name: ctg_max\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_max\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gap_pct:\n name: gap_pct\n description: The gap size percentage of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gap_pct\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_std:\n name: gc_std\n description: Standard deviation of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_std\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_avg:\n name: gc_avg\n description: Average of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_avg\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_input_reads:\n name: num_input_reads\n description: The sequence count number of input reads for assembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_input_reads\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_aligned_reads:\n name: num_aligned_reads\n description: The sequence count number of input reads aligned to assembled contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_aligned_reads\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n insdc_assembly_identifiers:\n name: insdc_assembly_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: assembly_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_assembly_identifiers\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: string\n pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeAssembly\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeAssembly\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetatranscriptomeAssembly\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetatranscriptomeAssembly\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetatranscriptomeAssembly\n\nA workflow process that provides expression values and read counts for gene features predicted on the contigs.
URI: nmdc:MetatranscriptomeExpressionAnalysis
classDiagram\n class MetatranscriptomeExpressionAnalysis\n click MetatranscriptomeExpressionAnalysis href \"../MetatranscriptomeExpressionAnalysis\"\n WorkflowExecution <|-- MetatranscriptomeExpressionAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetatranscriptomeExpressionAnalysis : alternative_identifiers\n\n MetatranscriptomeExpressionAnalysis : description\n\n MetatranscriptomeExpressionAnalysis : end_date\n\n MetatranscriptomeExpressionAnalysis : ended_at_time\n\n MetatranscriptomeExpressionAnalysis : execution_resource\n\n MetatranscriptomeExpressionAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetatranscriptomeExpressionAnalysis : git_url\n\n MetatranscriptomeExpressionAnalysis : has_failure_categorization\n\n MetatranscriptomeExpressionAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetatranscriptomeExpressionAnalysis : has_input\n\n MetatranscriptomeExpressionAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeExpressionAnalysis : has_output\n\n MetatranscriptomeExpressionAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeExpressionAnalysis : id\n\n MetatranscriptomeExpressionAnalysis : img_identifiers\n\n MetatranscriptomeExpressionAnalysis : name\n\n MetatranscriptomeExpressionAnalysis : processing_institution\n\n MetatranscriptomeExpressionAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetatranscriptomeExpressionAnalysis : protocol_link\n\n MetatranscriptomeExpressionAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetatranscriptomeExpressionAnalysis : qc_comment\n\n MetatranscriptomeExpressionAnalysis : qc_status\n\n MetatranscriptomeExpressionAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetatranscriptomeExpressionAnalysis : start_date\n\n MetatranscriptomeExpressionAnalysis : started_at_time\n\n MetatranscriptomeExpressionAnalysis : type\n\n MetatranscriptomeExpressionAnalysis : version\n\n MetatranscriptomeExpressionAnalysis : was_informed_by\n\n MetatranscriptomeExpressionAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetatranscriptomeExpressionAnalysis\ndescription: A workflow process that provides expression values and read counts for\n gene features predicted on the contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetatranscriptomeExpressionAnalysis\n\nname: MetatranscriptomeExpressionAnalysis\ndescription: A workflow process that provides expression values and read counts for\n gene features predicted on the contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n maximum_cardinality: 1\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetatranscriptomeExpressionAnalysis\n\nThe combining of components, particles or layers into a more homogeneous state.
__
URI: nmdc:MixingProcess
classDiagram\n class MixingProcess\n click MixingProcess href \"../MixingProcess\"\n MaterialProcessing <|-- MixingProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n MixingProcess : alternative_identifiers\n\n MixingProcess : description\n\n MixingProcess : duration\n\n MixingProcess --> \"0..1\" QuantityValue : duration\n click QuantityValue href \"../QuantityValue\"\n\n MixingProcess : end_date\n\n MixingProcess : has_failure_categorization\n\n MixingProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MixingProcess : has_input\n\n MixingProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n MixingProcess : has_output\n\n MixingProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n MixingProcess : id\n\n MixingProcess : instrument_used\n\n MixingProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n MixingProcess : name\n\n MixingProcess : processing_institution\n\n MixingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MixingProcess : protocol_link\n\n MixingProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MixingProcess : qc_comment\n\n MixingProcess : qc_status\n\n MixingProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MixingProcess : start_date\n\n MixingProcess : type\n\n\n\nname: MixingProcess\ndescription: 'The combining of components, particles or layers into a more homogeneous\n state.\n\n '\ncomments:\n- The mixing may be achieved manually or mechanically by shifting the material with\n stirrers or pumps or by revolving or shaking the container.\n- The process must not permit segregation of particles of different size or properties.\n- Homogeneity may be considered to have been achieved in a practical sense when the\n sampling error of the processed portion is negligible compared to the total error\n of the measurement system.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nis_a: MaterialProcessing\nslots:\n- duration\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The mixed sample.\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MixingProcess\n\nname: MixingProcess\ndescription: 'The combining of components, particles or layers into a more homogeneous\n state.\n\n '\ncomments:\n- The mixing may be achieved manually or mechanically by shifting the material with\n stirrers or pumps or by revolving or shaking the container.\n- The process must not permit segregation of particles of different size or properties.\n- Homogeneity may be considered to have been achieved in a practical sense when the\n sampling error of the processed portion is negligible compared to the total error\n of the measurement system.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The mixed sample.\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n duration:\n name: duration\n description: The elapsed time of an activity.\n examples:\n - value: JsonObj(has_numeric_value=2, has_unit='hours')\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: duration\n owner: MixingProcess\n domain_of:\n - MixingProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: MixingProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The mixed sample.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MixingProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MixingProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MixingProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MixingProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MixingProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MixingProcess\n\nA fluid mixture of substances that flow though a chromatographic stationary phase.
URI: nmdc:MobilePhaseSegment
classDiagram\n class MobilePhaseSegment\n click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n MobilePhaseSegment : duration\n\n MobilePhaseSegment --> \"0..1\" QuantityValue : duration\n click QuantityValue href \"../QuantityValue\"\n\n MobilePhaseSegment : substances_used\n\n MobilePhaseSegment --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n MobilePhaseSegment : type\n\n MobilePhaseSegment : volume\n\n MobilePhaseSegment --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: MobilePhaseSegment\ndescription: A fluid mixture of substances that flow though a chromatographic stationary\n phase.\ncomments:\n- Can be assembled into a list to account for a gradient.\n- Works best for separations that can be accounted for by a series of essentially\n linear changes in the mobile phase composition.\n- For gradients, each segment should declare it's duration.\n- For step-wise separations that might be implemented with a syringe and a cartridge,\n it will probably be more important to assert volumes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- duration\n- substances_used\n- type\n- volume\nclass_uri: nmdc:MobilePhaseSegment\n\nname: MobilePhaseSegment\ndescription: A fluid mixture of substances that flow though a chromatographic stationary\n phase.\ncomments:\n- Can be assembled into a list to account for a gradient.\n- Works best for separations that can be accounted for by a series of essentially\n linear changes in the mobile phase composition.\n- For gradients, each segment should declare it's duration.\n- For step-wise separations that might be implemented with a syringe and a cartridge,\n it will probably be more important to assert volumes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n duration:\n name: duration\n description: The elapsed time of an activity.\n examples:\n - value: JsonObj(has_numeric_value=2, has_unit='hours')\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: duration\n owner: MobilePhaseSegment\n domain_of:\n - MixingProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: QuantityValue\n substances_used:\n name: substances_used\n description: The substances that are combined to enable a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: MobilePhaseSegment\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MobilePhaseSegment\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n volume:\n name: volume\n description: The volume of a substance.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: MobilePhaseSegment\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\nclass_uri: nmdc:MobilePhaseSegment\n\nThe NMDC Schema is a foundational framework designed to standardize metadata for the National Microbiome Data Collaborative (NMDC) and collaborating data providors. By establishing a structured approach to metadata, the NMDC Schema enables researchers to organize, share, and interpret complex datasets with consistency and clarity. The NMDC Schema is critical substrate used to facilitate interoperability and collaboration, as it provide a common language for data exchange across systems and disciplines. In the context of the NMDC, this schema supports the integration of microbiome data from medicine, agriculture, bioenergy, and environmental science into a cohesive platform.
URI: https://w3id.org/nmdc/nmdc
"},{"location":"NamedThing/","title":"Class: NamedThing","text":"a databased entity or concept/class
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:NamedThing
classDiagram\n class NamedThing\n click NamedThing href \"../NamedThing\"\n NamedThing <|-- GeneProduct\n click GeneProduct href \"../GeneProduct\"\n NamedThing <|-- OntologyClass\n click OntologyClass href \"../OntologyClass\"\n NamedThing <|-- MaterialEntity\n click MaterialEntity href \"../MaterialEntity\"\n NamedThing <|-- PlannedProcess\n click PlannedProcess href \"../PlannedProcess\"\n NamedThing <|-- Study\n click Study href \"../Study\"\n NamedThing <|-- InformationObject\n click InformationObject href \"../InformationObject\"\n\n\n\n NamedThing : alternative_identifiers\n\n NamedThing : description\n\n NamedThing : id\n\n NamedThing : name\n\n NamedThing : type\n\n\n\nname: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- id\n- name\n- description\n- alternative_identifiers\n- type\nclass_uri: nmdc:NamedThing\n\nname: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: NamedThing\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NamedThing\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: NamedThing\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: NamedThing\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: NamedThing\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:NamedThing\n\nPrefix part of CURIE
URI: xsd:string
base: NCName
uri: xsd:string
repr: str
A URI, CURIE or BNODE that represents a node in a model.
URI: shex:nonLiteral
base: NodeIdentifier
uri: shex:nonLiteral
repr: str
URI: nmdc:NomAnalysis
classDiagram\n class NomAnalysis\n click NomAnalysis href \"../NomAnalysis\"\n WorkflowExecution <|-- NomAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n NomAnalysis : alternative_identifiers\n\n NomAnalysis : description\n\n NomAnalysis : end_date\n\n NomAnalysis : ended_at_time\n\n NomAnalysis : execution_resource\n\n NomAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n NomAnalysis : git_url\n\n NomAnalysis : has_failure_categorization\n\n NomAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n NomAnalysis : has_input\n\n NomAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n NomAnalysis : has_output\n\n NomAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n NomAnalysis : id\n\n NomAnalysis : name\n\n NomAnalysis : processing_institution\n\n NomAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n NomAnalysis : protocol_link\n\n NomAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n NomAnalysis : qc_comment\n\n NomAnalysis : qc_status\n\n NomAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n NomAnalysis : start_date\n\n NomAnalysis : started_at_time\n\n NomAnalysis : type\n\n NomAnalysis : uses_calibration\n\n NomAnalysis --> \"0..1\" CalibrationInformation : uses_calibration\n click CalibrationInformation href \"../CalibrationInformation\"\n\n NomAnalysis : version\n\n NomAnalysis : was_informed_by\n\n NomAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: NomAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- uses_calibration\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:NomAnalysis\n\nname: NomAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n uses_calibration:\n name: uses_calibration\n description: calibration information is used by a process\n comments:\n - Retenion index calibration data generated by a gas chromatography mass spectromery\n run is used when analyzing metabolomics data\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: uses_calibration\n owner: NomAnalysis\n domain_of:\n - MetabolomicsAnalysis\n - NomAnalysis\n range: CalibrationInformation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: NomAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NomAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: NomAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: NomAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: NomAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:NomAnalysis\n\nA DataGeneration in which the sequence of DNA or RNA molecules is generated.
URI: nmdc:NucleotideSequencing
classDiagram\n class NucleotideSequencing\n click NucleotideSequencing href \"../NucleotideSequencing\"\n DataGeneration <|-- NucleotideSequencing\n click DataGeneration href \"../DataGeneration\"\n\n\n\n NucleotideSequencing : add_date\n\n NucleotideSequencing : alternative_identifiers\n\n NucleotideSequencing : analyte_category\n\n NucleotideSequencing --> \"1\" NucleotideSequencingEnum : analyte_category\n click NucleotideSequencingEnum href \"../NucleotideSequencingEnum\"\n\n NucleotideSequencing : associated_studies\n\n NucleotideSequencing --> \"1..*\" Study : associated_studies\n click Study href \"../Study\"\n\n NucleotideSequencing : description\n\n NucleotideSequencing : end_date\n\n NucleotideSequencing : gold_sequencing_project_identifiers\n\n NucleotideSequencing : has_failure_categorization\n\n NucleotideSequencing --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n NucleotideSequencing : has_input\n\n NucleotideSequencing --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n NucleotideSequencing : has_output\n\n NucleotideSequencing --> \"*\" DataObject : has_output\n click DataObject href \"../DataObject\"\n\n NucleotideSequencing : id\n\n NucleotideSequencing : insdc_bioproject_identifiers\n\n NucleotideSequencing : insdc_experiment_identifiers\n\n NucleotideSequencing : instrument_used\n\n NucleotideSequencing --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n NucleotideSequencing : mod_date\n\n NucleotideSequencing : name\n\n NucleotideSequencing : ncbi_project_name\n\n NucleotideSequencing : principal_investigator\n\n NucleotideSequencing --> \"0..1\" PersonValue : principal_investigator\n click PersonValue href \"../PersonValue\"\n\n NucleotideSequencing : processing_institution\n\n NucleotideSequencing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n NucleotideSequencing : protocol_link\n\n NucleotideSequencing --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n NucleotideSequencing : qc_comment\n\n NucleotideSequencing : qc_status\n\n NucleotideSequencing --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n NucleotideSequencing : start_date\n\n NucleotideSequencing : target_gene\n\n NucleotideSequencing --> \"0..1\" TargetGeneEnum : target_gene\n click TargetGeneEnum href \"../TargetGeneEnum\"\n\n NucleotideSequencing : target_subfragment\n\n NucleotideSequencing --> \"0..1\" TextValue : target_subfragment\n click TextValue href \"../TextValue\"\n\n NucleotideSequencing : type\n\n\n\nname: NucleotideSequencing\ndescription: A DataGeneration in which the sequence of DNA or RNA molecules is generated.\ncomments:\n- For example data generated from an Illumina or Pacific Biosciences instrument.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: DataGeneration\nslots:\n- gold_sequencing_project_identifiers\n- insdc_bioproject_identifiers\n- insdc_experiment_identifiers\n- ncbi_project_name\n- target_gene\n- target_subfragment\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n analyte_category:\n name: analyte_category\n range: NucleotideSequencingEnum\nclass_uri: nmdc:NucleotideSequencing\n\nname: NucleotideSequencing\ndescription: A DataGeneration in which the sequence of DNA or RNA molecules is generated.\ncomments:\n- For example data generated from an Illumina or Pacific Biosciences instrument.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: DataGeneration\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n analyte_category:\n name: analyte_category\n range: NucleotideSequencingEnum\nattributes:\n gold_sequencing_project_identifiers:\n name: gold_sequencing_project_identifiers\n description: identifiers for corresponding sequencing project in GOLD\n examples:\n - value: https://bioregistry.io/gold:Gp0108335\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: omics_processing_identifiers\n mixins:\n - gold_identifiers\n alias: gold_sequencing_project_identifiers\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n range: external_identifier\n multivalued: true\n pattern: ^gold:Gp[0-9]+$\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n description: identifiers for corresponding project in INSDC Bioproject\n comments:\n - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n one to one\n examples:\n - value: https://bioregistry.io/bioproject:PRJNA366857\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2\n metatranscriptome\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ncbi.nlm.nih.gov/bioproject/\n - https://www.ddbj.nig.ac.jp/bioproject/index-e.html\n aliases:\n - NCBI bioproject identifiers\n - DDBJ bioproject identifiers\n rank: 1000\n is_a: study_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_bioproject_identifiers\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n insdc_experiment_identifiers:\n name: insdc_experiment_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_experiment_identifiers\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n - DataObject\n range: external_identifier\n multivalued: true\n pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n ncbi_project_name:\n name: ncbi_project_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_project_name\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n range: string\n target_gene:\n name: target_gene\n annotations:\n expected_value:\n tag: expected_value\n value: gene name\n description: Targeted gene or locus name for marker gene studies\n title: target gene\n examples:\n - value: 16S rRNA, 18S rRNA, nif, amoA, rpo\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target gene\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000044\n alias: target_gene\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n range: TargetGeneEnum\n multivalued: false\n target_subfragment:\n name: target_subfragment\n annotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\n description: Name of subfragment of a gene or locus. Important to e.g. identify\n special regions on marker genes like V6 on 16S rRNA\n title: target subfragment\n examples:\n - value: V6, V9, ITS\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target subfragment\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000045\n alias: target_subfragment\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n range: TextValue\n multivalued: false\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: NucleotideSequencing\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n analyte_category:\n name: analyte_category\n description: \"The type of analyte(s) that were measured in the data generation\\\n \\ process and analyzed\\n in the Workflow Chain\\n\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: analyte_category\n owner: NucleotideSequencing\n domain_of:\n - DataGeneration\n range: NucleotideSequencingEnum\n required: true\n associated_studies:\n name: associated_studies\n description: The study associated with a resource.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: associated_studies\n owner: NucleotideSequencing\n domain_of:\n - Biosample\n - DataGeneration\n range: Study\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: NucleotideSequencing\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: NucleotideSequencing\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n alias: principal_investigator\n owner: NucleotideSequencing\n domain_of:\n - Study\n - DataGeneration\n range: PersonValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: DataObject\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: NucleotideSequencing\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NucleotideSequencing\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: NucleotideSequencing\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: NucleotideSequencing\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: NucleotideSequencing\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:NucleotideSequencing\n\nURI: NucleotideSequencingEnum
"},{"location":"NucleotideSequencingEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metagenome None metatranscriptome None amplicon_sequencing_assay OBI:0002767"},{"location":"NucleotideSequencingEnum/#slots","title":"Slots","text":"Name Description analyte_category"},{"location":"NucleotideSequencingEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NucleotideSequencingEnum/#schema-source","title":"Schema Source","text":"name: NucleotideSequencingEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metagenome:\n text: metagenome\n title: Metagenome\n aliases:\n - metaG\n metatranscriptome:\n text: metatranscriptome\n title: Metatranscriptome\n aliases:\n - metaT\n amplicon_sequencing_assay:\n text: amplicon_sequencing_assay\n meaning: OBI:0002767\n title: Amplicon\n\nA URI or CURIE that represents an object in the model.
URI: shex:iri
base: ElementIdentifier
uri: shex:iri
repr: str
URI: OccupDocumentEnum
"},{"location":"OccupDocumentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description automated count None estimate None manual count None videos None"},{"location":"OccupDocumentEnum/#slots","title":"Slots","text":"Name Description occup_document The type of documentation of occupancy"},{"location":"OccupDocumentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OccupDocumentEnum/#schema-source","title":"Schema Source","text":"name: occup_document_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n automated count:\n text: automated count\n estimate:\n text: estimate\n manual count:\n text: manual count\n videos:\n text: videos\n\nA representation of class defined in an external ontology.
URI: nmdc:OntologyClass
classDiagram\n class OntologyClass\n click OntologyClass href \"../OntologyClass\"\n NamedThing <|-- OntologyClass\n click NamedThing href \"../NamedThing\"\n\n\n OntologyClass <|-- EnvironmentalMaterialTerm\n click EnvironmentalMaterialTerm href \"../EnvironmentalMaterialTerm\"\n OntologyClass <|-- ChemicalEntity\n click ChemicalEntity href \"../ChemicalEntity\"\n OntologyClass <|-- FunctionalAnnotationTerm\n click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n OntologyClass : alternative_identifiers\n\n OntologyClass : alternative_names\n\n OntologyClass : definition\n\n OntologyClass : description\n\n OntologyClass : id\n\n OntologyClass : name\n\n OntologyClass : relations\n\n OntologyClass --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n OntologyClass : type\n\n\n\nname: OntologyClass\ndescription: A representation of class defined in an external ontology.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:OntologyClass\n- owl:Class\n- schema:Class\nis_a: NamedThing\nslots:\n- alternative_names\nslot_usage:\n id:\n name: id\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nattributes:\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\nclass_uri: nmdc:OntologyClass\n\nname: OntologyClass\ndescription: A representation of class defined in an external ontology.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:OntologyClass\n- owl:Class\n- schema:Class\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nattributes:\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: OntologyClass\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: OntologyClass\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: OntologyClass\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: OntologyClass\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OntologyClass\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OntologyClass\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: OntologyClass\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: OntologyClass\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:OntologyClass\n\nA relationship between two ontology classes as specified either directly in the ontology in the form of axioms (statements or assertions that defines rules or constraints in an ontology) or inferred via reasoning. The association object is defined by two terms (the subject and the object) and the relationship between them (the predicate). Because ontologies often have a plethora of relationships/axiom types and can have additional metadata on the relationship itself, these kinds of relationships are structured as a class instead of a simple set of slots on OntologyClass itself.
URI: nmdc:OntologyRelation
classDiagram\n class OntologyRelation\n click OntologyRelation href \"../OntologyRelation\"\n\n OntologyRelation : object\n\n OntologyRelation --> \"1\" OntologyClass : object\n click OntologyClass href \"../OntologyClass\"\n\n OntologyRelation : predicate\n\n OntologyRelation --> \"1\" OntologyClass : predicate\n click OntologyClass href \"../OntologyClass\"\n\n OntologyRelation : subject\n\n OntologyRelation --> \"1\" OntologyClass : subject\n click OntologyClass href \"../OntologyClass\"\n\n OntologyRelation : type\n\n\n\nOntologyClass as defined below). Not all ontology axioms (associations) between terms need to be ingested into the NMDC data stores. In general, subclass_of and part_of relationships/axioms are often good default relations/associations to support ontology browsing in user interfaces.name: OntologyRelation\ndescription: A relationship between two ontology classes as specified either directly\n in the ontology in the form of axioms (statements or assertions that defines rules\n or constraints in an ontology) or inferred via reasoning. The association object\n is defined by two terms (the subject and the object) and the relationship between\n them (the predicate). Because ontologies often have a plethora of relationships/axiom\n types and can have additional metadata on the relationship itself, these kinds of\n relationships are structured as a class instead of a simple set of slots on OntologyClass\n itself.\ncomments:\n- 'For example, the relationship between ''soil'' and ''enriched soil'' in the Environmental\n Ontology (ENVO) is defined by the following axioms: ''enriched soil'' subclass_of\n ''soil'', and ''enriched soil'' has_increased_levels_of (some) ''material entity.'' Converting\n these stat\u2202ements to OntologyAssociations so they can be used in the NMDC data\n stores, the subject of the first axiom or statement, would be ''soil'', the predicate\n would be ''subclass_of'', and the object would be ''enriched soil''. For the second\n axiom, the subject would be ''enriched soil'', the predicate would be ''has_increased_levels_of'',\n and the object would be ''material entity.'' (Note that text labels are used in\n this example for ease of understanding and the literal values of subject, predicate,\n and object in this class will be the id (curie) of the `OntologyClass` as defined\n below). Not all ontology axioms (associations) between terms need to be ingested\n into the NMDC data stores. In general, subclass_of and part_of relationships/axioms\n are often good default relations/associations to support ontology browsing in user\n interfaces.'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OntologyAssociation\nslots:\n- type\nattributes:\n subject:\n name: subject\n from_schema: https://w3id.org/nmdc/basic_classes\n domain_of:\n - FunctionalAnnotation\n - OntologyRelation\n range: OntologyClass\n required: true\n predicate:\n name: predicate\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n domain_of:\n - OntologyRelation\n range: OntologyClass\n required: true\n object:\n name: object\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n domain_of:\n - OntologyRelation\n range: OntologyClass\n required: true\nclass_uri: nmdc:OntologyRelation\n\nname: OntologyRelation\ndescription: A relationship between two ontology classes as specified either directly\n in the ontology in the form of axioms (statements or assertions that defines rules\n or constraints in an ontology) or inferred via reasoning. The association object\n is defined by two terms (the subject and the object) and the relationship between\n them (the predicate). Because ontologies often have a plethora of relationships/axiom\n types and can have additional metadata on the relationship itself, these kinds of\n relationships are structured as a class instead of a simple set of slots on OntologyClass\n itself.\ncomments:\n- 'For example, the relationship between ''soil'' and ''enriched soil'' in the Environmental\n Ontology (ENVO) is defined by the following axioms: ''enriched soil'' subclass_of\n ''soil'', and ''enriched soil'' has_increased_levels_of (some) ''material entity.'' Converting\n these stat\u2202ements to OntologyAssociations so they can be used in the NMDC data\n stores, the subject of the first axiom or statement, would be ''soil'', the predicate\n would be ''subclass_of'', and the object would be ''enriched soil''. For the second\n axiom, the subject would be ''enriched soil'', the predicate would be ''has_increased_levels_of'',\n and the object would be ''material entity.'' (Note that text labels are used in\n this example for ease of understanding and the literal values of subject, predicate,\n and object in this class will be the id (curie) of the `OntologyClass` as defined\n below). Not all ontology axioms (associations) between terms need to be ingested\n into the NMDC data stores. In general, subclass_of and part_of relationships/axioms\n are often good default relations/associations to support ontology browsing in user\n interfaces.'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OntologyAssociation\nattributes:\n subject:\n name: subject\n from_schema: https://w3id.org/nmdc/basic_classes\n alias: subject\n owner: OntologyRelation\n domain_of:\n - FunctionalAnnotation\n - OntologyRelation\n range: OntologyClass\n required: true\n predicate:\n name: predicate\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: predicate\n owner: OntologyRelation\n domain_of:\n - OntologyRelation\n range: OntologyClass\n required: true\n object:\n name: object\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: object\n owner: OntologyRelation\n domain_of:\n - OntologyRelation\n range: OntologyClass\n required: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: OntologyRelation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:OntologyRelation\n\nURI: OrganismCountEnum
"},{"location":"OrganismCountEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ATP None MPN None other None"},{"location":"OrganismCountEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OrganismCountEnum/#schema-source","title":"Schema Source","text":"name: organism_count_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n ATP:\n text: ATP\n MPN:\n text: MPN\n other:\n text: other\n\nA set of genes or gene products in which all members are orthologous
URI: nmdc:OrthologyGroup
classDiagram\n class OrthologyGroup\n click OrthologyGroup href \"../OrthologyGroup\"\n FunctionalAnnotationTerm <|-- OrthologyGroup\n click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n OrthologyGroup : alternative_identifiers\n\n OrthologyGroup : alternative_names\n\n OrthologyGroup : definition\n\n OrthologyGroup : description\n\n OrthologyGroup : id\n\n OrthologyGroup : name\n\n OrthologyGroup : relations\n\n OrthologyGroup --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n OrthologyGroup : type\n\n\n\nInstances of this class should have identifiers with one of the following prefixes:
CATH
EGGNOG
KEGG.ORTHOLOGY
PANTHER.FAMILY
PFAM
SUPFAM
TIGRFAM
name: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\ntodos:\n- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable\n in the Data Portal?\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nclass_uri: nmdc:OrthologyGroup\n\nname: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\ntodos:\n- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable\n in the Data Portal?\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nattributes:\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: OrthologyGroup\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: OrthologyGroup\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: OrthologyGroup\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: OrthologyGroup\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OrthologyGroup\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OrthologyGroup\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: OrthologyGroup\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: OrthologyGroup\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:OrthologyGroup\n\nURI: OxyStatSampEnum
"},{"location":"OxyStatSampEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aerobic None anaerobic None other None"},{"location":"OxyStatSampEnum/#slots","title":"Slots","text":"Name Description oxy_stat_samp Oxygenation status of sample"},{"location":"OxyStatSampEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OxyStatSampEnum/#schema-source","title":"Schema Source","text":"name: oxy_stat_samp_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n aerobic:\n text: aerobic\n anaerobic:\n text: anaerobic\n other:\n text: other\n\nA pathway is a sequence of steps/reactions carried out by an organism or community of organisms
URI: nmdc:Pathway
classDiagram\n class Pathway\n click Pathway href \"../Pathway\"\n FunctionalAnnotationTerm <|-- Pathway\n click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n Pathway : alternative_identifiers\n\n Pathway : alternative_names\n\n Pathway : definition\n\n Pathway : description\n\n Pathway : id\n\n Pathway : name\n\n Pathway : relations\n\n Pathway --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n Pathway : type\n\n\n\nInstances of this class should have identifiers with one of the following prefixes:
KEGG_PATHWAY
COG
name: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n or community of organisms\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\ntodos:\n- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable\n part_of a Pathway\n- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in\n the Data Portal?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nclass_uri: nmdc:Pathway\n\nname: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n or community of organisms\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\ntodos:\n- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable\n part_of a Pathway\n- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in\n the Data Portal?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nattributes:\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: Pathway\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: Pathway\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: Pathway\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Pathway\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Pathway\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Pathway\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Pathway\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Pathway\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Pathway\n\nThis is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information
URI: nmdc:PeptideQuantification
classDiagram\n class PeptideQuantification\n click PeptideQuantification href \"../PeptideQuantification\"\n\n PeptideQuantification : all_proteins\n\n PeptideQuantification --> \"*\" GeneProduct : all_proteins\n click GeneProduct href \"../GeneProduct\"\n\n PeptideQuantification : best_protein\n\n PeptideQuantification --> \"0..1\" GeneProduct : best_protein\n click GeneProduct href \"../GeneProduct\"\n\n PeptideQuantification : min_q_value\n\n PeptideQuantification : peptide_sequence\n\n PeptideQuantification : peptide_spectral_count\n\n PeptideQuantification : peptide_sum_masic_abundance\n\n PeptideQuantification : type\n\n\n\nname: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n peptide sequence and related information\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- type\n- all_proteins\n- best_protein\n- min_q_value\n- peptide_sequence\n- peptide_spectral_count\n- peptide_sum_masic_abundance\nclass_uri: nmdc:PeptideQuantification\n\nname: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n peptide sequence and related information\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: PeptideQuantification\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n all_proteins:\n name: all_proteins\n description: the list of protein identifiers that are associated with the peptide\n sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: all_proteins\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n multivalued: true\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly associated with the\n peptide sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: best_protein\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n min_q_value:\n name: min_q_value\n description: smallest Q-Value associated with the peptide sequence as provided\n by MSGFPlus tool\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - OBI:0001442\n rank: 1000\n alias: min_q_value\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: float\n peptide_sequence:\n name: peptide_sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sequence\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: string\n peptide_spectral_count:\n name: peptide_spectral_count\n description: sum of filter passing MS2 spectra associated with the peptide sequence\n within a given LC-MS/MS data file\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_spectral_count\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: integer\n peptide_sum_masic_abundance:\n name: peptide_sum_masic_abundance\n description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n associated with the peptide sequence from a given LC-MS/MS data file using the\n MASIC tool\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sum_masic_abundance\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: integer\nclass_uri: nmdc:PeptideQuantification\n\nAn attribute value representing a person
URI: nmdc:PersonValue
classDiagram\n class PersonValue\n click PersonValue href \"../PersonValue\"\n AttributeValue <|-- PersonValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n PersonValue : email\n\n PersonValue : has_raw_value\n\n PersonValue : name\n\n PersonValue : orcid\n\n PersonValue : profile_image_url\n\n PersonValue : type\n\n PersonValue : websites\n\n\n\nname: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- email\n- name\n- orcid\n- profile_image_url\n- websites\nslot_usage:\n orcid:\n name: orcid\n annotations:\n tooltip:\n tag: tooltip\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n email:\n name: email\n annotations:\n tooltip:\n tag: tooltip\n value: Email address for this person.\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\nclass_uri: nmdc:PersonValue\n\nname: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslot_usage:\n orcid:\n name: orcid\n annotations:\n tooltip:\n tag: tooltip\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n email:\n name: email\n annotations:\n tooltip:\n tag: tooltip\n value: Email address for this person.\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\nattributes:\n email:\n name: email\n annotations:\n tooltip:\n tag: tooltip\n value: Email address for this person.\n description: An email address for an entity such as a person. This should be the\n primary email address used.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: schema:email\n alias: email\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: PersonValue\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n orcid:\n name: orcid\n annotations:\n tooltip:\n tag: tooltip\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n description: The ORCID of a person.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: orcid\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n profile_image_url:\n name: profile_image_url\n description: A url that points to an image of a person.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: profile_image_url\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n websites:\n name: websites\n description: A list of websites that are associated with the entity.\n comments:\n - DOIs should not be included as websites. Instead, use the associated_dois slot.\n - A consortium's homepage website should be included in the homepage_website slot,\n not in websites.\n - consortium is a convenience term for a Study whose study_category value is consortium\n - the website slot and its subproperties are virtually identical to the url slot,\n except that they are multivalued and url is single-valued.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:url\n rank: 1000\n alias: websites\n owner: PersonValue\n domain_of:\n - PersonValue\n - Study\n range: string\n multivalued: true\n pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: PersonValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: PersonValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:PersonValue\n\nNote
This is an abstract class and should not be instantiated directly.
URI: OBI:0000011
classDiagram\n class PlannedProcess\n click PlannedProcess href \"../PlannedProcess\"\n NamedThing <|-- PlannedProcess\n click NamedThing href \"../NamedThing\"\n\n\n PlannedProcess <|-- CollectingBiosamplesFromSite\n click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n PlannedProcess <|-- ProtocolExecution\n click ProtocolExecution href \"../ProtocolExecution\"\n PlannedProcess <|-- StorageProcess\n click StorageProcess href \"../StorageProcess\"\n PlannedProcess <|-- MaterialProcessing\n click MaterialProcessing href \"../MaterialProcessing\"\n PlannedProcess <|-- DataGeneration\n click DataGeneration href \"../DataGeneration\"\n PlannedProcess <|-- WorkflowExecution\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n PlannedProcess : alternative_identifiers\n\n PlannedProcess : description\n\n PlannedProcess : end_date\n\n PlannedProcess : has_failure_categorization\n\n PlannedProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n PlannedProcess : has_input\n\n PlannedProcess --> \"*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n PlannedProcess : has_output\n\n PlannedProcess --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n PlannedProcess : id\n\n PlannedProcess : name\n\n PlannedProcess : processing_institution\n\n PlannedProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n PlannedProcess : protocol_link\n\n PlannedProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n PlannedProcess : qc_comment\n\n PlannedProcess : qc_status\n\n PlannedProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n PlannedProcess : start_date\n\n PlannedProcess : type\n\n\n\nname: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nslots:\n- has_input\n- has_output\n- processing_institution\n- protocol_link\n- start_date\n- end_date\n- qc_status\n- qc_comment\n- has_failure_categorization\nclass_uri: OBI:0000011\n\nname: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nattributes:\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: PlannedProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: PlannedProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: PlannedProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: PlannedProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: PlannedProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: OBI:0000011\n\nURI: PlantGrowthMedEnum
"},{"location":"PlantGrowthMedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description other artificial liquid medium None other artificial solid medium None peat moss None perlite None pumice None sand None soil None vermiculite None water None"},{"location":"PlantGrowthMedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantGrowthMedEnum/#schema-source","title":"Schema Source","text":"name: plant_growth_med_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n other artificial liquid medium:\n text: other artificial liquid medium\n other artificial solid medium:\n text: other artificial solid medium\n peat moss:\n text: peat moss\n perlite:\n text: perlite\n pumice:\n text: pumice\n sand:\n text: sand\n soil:\n text: soil\n vermiculite:\n text: vermiculite\n water:\n text: water\n\nURI: PlantSexEnum
"},{"location":"PlantSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Androdioecious None Androecious None Androgynous None Androgynomonoecious None Andromonoecious None Bisexual None Dichogamous None Diclinous None Dioecious None Gynodioecious None Gynoecious None Gynomonoecious None Hermaphroditic None Imperfect None Monoclinous None Monoecious None Perfect None Polygamodioecious None Polygamomonoecious None Polygamous None Protandrous None Protogynous None Subandroecious None Subdioecious None Subgynoecious None Synoecious None Trimonoecious None Trioecious None Unisexual None"},{"location":"PlantSexEnum/#slots","title":"Slots","text":"Name Description plant_sex Sex of the reproductive parts on the whole plant, e"},{"location":"PlantSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantSexEnum/#schema-source","title":"Schema Source","text":"name: plant_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Androdioecious:\n text: Androdioecious\n Androecious:\n text: Androecious\n Androgynous:\n text: Androgynous\n Androgynomonoecious:\n text: Androgynomonoecious\n Andromonoecious:\n text: Andromonoecious\n Bisexual:\n text: Bisexual\n Dichogamous:\n text: Dichogamous\n Diclinous:\n text: Diclinous\n Dioecious:\n text: Dioecious\n Gynodioecious:\n text: Gynodioecious\n Gynoecious:\n text: Gynoecious\n Gynomonoecious:\n text: Gynomonoecious\n Hermaphroditic:\n text: Hermaphroditic\n Imperfect:\n text: Imperfect\n Monoclinous:\n text: Monoclinous\n Monoecious:\n text: Monoecious\n Perfect:\n text: Perfect\n Polygamodioecious:\n text: Polygamodioecious\n Polygamomonoecious:\n text: Polygamomonoecious\n Polygamous:\n text: Polygamous\n Protandrous:\n text: Protandrous\n Protogynous:\n text: Protogynous\n Subandroecious:\n text: Subandroecious\n Subdioecious:\n text: Subdioecious\n Subgynoecious:\n text: Subgynoecious\n Synoecious:\n text: Synoecious\n Trimonoecious:\n text: Trimonoecious\n Trioecious:\n text: Trioecious\n Unisexual:\n text: Unisexual\n\nURI: PolarityModeEnum
"},{"location":"PolarityModeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description positive None negative None"},{"location":"PolarityModeEnum/#slots","title":"Slots","text":"Name Description polarity_mode the polarity of which ions are generated and detected"},{"location":"PolarityModeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PolarityModeEnum/#schema-source","title":"Schema Source","text":"name: PolarityModeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n positive:\n text: positive\n negative:\n text: negative\n\nphysical combination of several instances of like material.
URI: nmdc:Pooling
classDiagram\n class Pooling\n click Pooling href \"../Pooling\"\n MaterialProcessing <|-- Pooling\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n Pooling : alternative_identifiers\n\n Pooling : description\n\n Pooling : end_date\n\n Pooling : has_failure_categorization\n\n Pooling --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n Pooling : has_input\n\n Pooling --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n Pooling : has_output\n\n Pooling --> \"1..*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n Pooling : id\n\n Pooling : instrument_used\n\n Pooling --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n Pooling : name\n\n Pooling : processing_institution\n\n Pooling --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n Pooling : protocol_link\n\n Pooling --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n Pooling : qc_comment\n\n Pooling : qc_status\n\n Pooling --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n Pooling : start_date\n\n Pooling : type\n\n\n\nname: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: MaterialProcessing\nslot_usage:\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 2\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 1\n maximum_cardinality: 1\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:Pooling\n\nname: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: MaterialProcessing\nslot_usage:\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 2\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 1\n maximum_cardinality: 1\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: Pooling\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 2\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 1\n maximum_cardinality: 1\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Pooling\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Pooling\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Pooling\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Pooling\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Pooling\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Pooling\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Pooling\n\nA portion of any matter of defined composition that has discrete existence, whose origin may be biological, mineral or chemical.
URI: nmdc:PortionOfSubstance
classDiagram\n class PortionOfSubstance\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n PortionOfSubstance : final_concentration\n\n PortionOfSubstance --> \"0..1\" QuantityValue : final_concentration\n click QuantityValue href \"../QuantityValue\"\n\n PortionOfSubstance : known_as\n\n PortionOfSubstance --> \"0..1\" ChemicalEntityEnum : known_as\n click ChemicalEntityEnum href \"../ChemicalEntityEnum\"\n\n PortionOfSubstance : mass\n\n PortionOfSubstance --> \"0..1\" QuantityValue : mass\n click QuantityValue href \"../QuantityValue\"\n\n PortionOfSubstance : sample_state_information\n\n PortionOfSubstance --> \"0..1\" SampleStateEnum : sample_state_information\n click SampleStateEnum href \"../SampleStateEnum\"\n\n PortionOfSubstance : source_concentration\n\n PortionOfSubstance --> \"0..1\" QuantityValue : source_concentration\n click QuantityValue href \"../QuantityValue\"\n\n PortionOfSubstance : substance_role\n\n PortionOfSubstance --> \"0..1\" SubstanceRoleEnum : substance_role\n click SubstanceRoleEnum href \"../SubstanceRoleEnum\"\n\n PortionOfSubstance : type\n\n PortionOfSubstance : volume\n\n PortionOfSubstance --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: PortionOfSubstance\ndescription: A portion of any matter of defined composition that has discrete existence,\n whose origin may be biological, mineral or chemical.\ntitle: Portion of a Substance\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:Substance\nslots:\n- final_concentration\n- mass\n- sample_state_information\n- source_concentration\n- known_as\n- substance_role\n- type\n- volume\nclass_uri: nmdc:PortionOfSubstance\n\nname: PortionOfSubstance\ndescription: A portion of any matter of defined composition that has discrete existence,\n whose origin may be biological, mineral or chemical.\ntitle: Portion of a Substance\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:Substance\nattributes:\n final_concentration:\n name: final_concentration\n description: When solutions A (containing substance X) and B are combined together,\n this slot captures the concentration of X in the combination\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: concentration\n alias: final_concentration\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: QuantityValue\n mass:\n name: mass\n description: A physical quality that inheres in a bearer by virtue of the proportion\n of the bearer's amount of matter.\n title: mass\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - PATO:0000125\n rank: 1000\n alias: mass\n owner: PortionOfSubstance\n domain_of:\n - SubSamplingProcess\n - PortionOfSubstance\n range: QuantityValue\n sample_state_information:\n name: sample_state_information\n description: The chemical phase of a pure sample, or the state of a mixed sample\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sample_state_information\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: SampleStateEnum\n source_concentration:\n name: source_concentration\n description: When solutions A (containing substance X) and B are combined together,\n this slot captures the concentration of X in solution A\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: concentration\n alias: source_concentration\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: QuantityValue\n known_as:\n name: known_as\n description: The substance from which a portion was taken.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: known_as\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: ChemicalEntityEnum\n substance_role:\n name: substance_role\n description: The role of a substance in a process\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substance_role\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: SubstanceRoleEnum\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: PortionOfSubstance\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n volume:\n name: volume\n description: The volume of a substance.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: PortionOfSubstance\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\nclass_uri: nmdc:PortionOfSubstance\n\nURI: nmdc:ProcessedSample
classDiagram\n class ProcessedSample\n click ProcessedSample href \"../ProcessedSample\"\n Sample <|-- ProcessedSample\n click Sample href \"../Sample\"\n\n\n\n ProcessedSample : alternative_identifiers\n\n ProcessedSample : biomaterial_purity\n\n ProcessedSample --> \"0..1\" QuantityValue : biomaterial_purity\n click QuantityValue href \"../QuantityValue\"\n\n ProcessedSample : description\n\n ProcessedSample : dna_absorb1\n\n ProcessedSample : dna_concentration\n\n ProcessedSample : external_database_identifiers\n\n ProcessedSample : id\n\n ProcessedSample : name\n\n ProcessedSample : type\n\n\n\nname: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Sample\nslots:\n- biomaterial_purity\n- dna_absorb1\n- dna_concentration\n- external_database_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ProcessedSample\n\nname: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Sample\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n biomaterial_purity:\n name: biomaterial_purity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: biomaterial_purity\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: QuantityValue\n dna_absorb1:\n name: dna_absorb1\n description: 260/280 measurement of DNA sample purity\n title: DNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n alias: dna_absorb1\n owner: ProcessedSample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_concentration:\n name: dna_concentration\n title: DNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n alias: dna_concentration\n owner: ProcessedSample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n external_database_identifiers:\n name: external_database_identifiers\n description: Link to corresponding identifier in external database\n notes:\n - had tried ranges of external identifier and string\n comments:\n - The value of this field is always a registered CURIE\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - skos:closeMatch\n rank: 1000\n is_a: alternative_identifiers\n abstract: true\n alias: external_database_identifiers\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ProcessedSample\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ProcessedSample\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ProcessedSample\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ProcessedSample\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ProcessedSample\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ProcessedSample\n\nURI: ProcessingInstitutionEnum
"},{"location":"ProcessingInstitutionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UCSD https://ror.org/0168r3w48 JGI https://ror.org/04xm1d337 EMSL https://ror.org/04rc0xn13 Battelle https://ror.org/01h5tnr73 ANL https://ror.org/05gvnxz63 UCD_Genome_Center https://genomecenter.ucdavis.edu/ Azenta https://www.azenta.com/"},{"location":"ProcessingInstitutionEnum/#slots","title":"Slots","text":"Name Description processing_institution The organization that processed the sample"},{"location":"ProcessingInstitutionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProcessingInstitutionEnum/#schema-source","title":"Schema Source","text":"name: ProcessingInstitutionEnum\nnotes:\n- use ROR meanings like https://ror.org/0168r3w48 for UCSD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n UCSD:\n text: UCSD\n meaning: https://ror.org/0168r3w48\n title: University of California, San Diego\n JGI:\n text: JGI\n meaning: https://ror.org/04xm1d337\n title: Joint Genome Institute\n EMSL:\n text: EMSL\n meaning: https://ror.org/04rc0xn13\n title: Environmental Molecular Sciences Laboratory\n aliases:\n - Environmental Molecular Science Laboratory\n - Environmental Molecular Sciences Lab\n Battelle:\n text: Battelle\n meaning: https://ror.org/01h5tnr73\n title: Battelle Memorial Institute\n ANL:\n text: ANL\n meaning: https://ror.org/05gvnxz63\n title: Argonne National Laboratory\n UCD_Genome_Center:\n text: UCD_Genome_Center\n meaning: https://genomecenter.ucdavis.edu/\n title: University of California, Davis Genome Center\n Azenta:\n text: Azenta\n meaning: https://www.azenta.com/\n title: Azenta Life Sciences\n\nURI: ProfilePositionEnum
"},{"location":"ProfilePositionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description summit None shoulder None backslope None footslope None toeslope None"},{"location":"ProfilePositionEnum/#slots","title":"Slots","text":"Name Description profile_position Cross-sectional position in the hillslope where sample was collected"},{"location":"ProfilePositionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProfilePositionEnum/#schema-source","title":"Schema Source","text":"name: profile_position_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n summit:\n text: summit\n shoulder:\n text: shoulder\n backslope:\n text: backslope\n footslope:\n text: footslope\n toeslope:\n text: toeslope\n\nThis is used to link a metaproteomics analysis workflow to a specific protein
URI: nmdc:ProteinQuantification
classDiagram\n class ProteinQuantification\n click ProteinQuantification href \"../ProteinQuantification\"\n\n ProteinQuantification : all_proteins\n\n ProteinQuantification --> \"*\" GeneProduct : all_proteins\n click GeneProduct href \"../GeneProduct\"\n\n ProteinQuantification : best_protein\n\n ProteinQuantification --> \"0..1\" GeneProduct : best_protein\n click GeneProduct href \"../GeneProduct\"\n\n ProteinQuantification : peptide_sequence_count\n\n ProteinQuantification : protein_spectral_count\n\n ProteinQuantification : protein_sum_masic_abundance\n\n ProteinQuantification : type\n\n\n\nname: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n protein\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- all_proteins\n- best_protein\n- peptide_sequence_count\n- protein_spectral_count\n- protein_sum_masic_abundance\n- type\nclass_uri: nmdc:ProteinQuantification\n\nname: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n protein\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n all_proteins:\n name: all_proteins\n description: the list of protein identifiers that are associated with the peptide\n sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: all_proteins\n owner: ProteinQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n multivalued: true\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly associated with the\n peptide sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: best_protein\n owner: ProteinQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n peptide_sequence_count:\n name: peptide_sequence_count\n description: count of peptide sequences grouped to the best_protein\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sequence_count\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n protein_spectral_count:\n name: protein_spectral_count\n description: sum of filter passing MS2 spectra associated with the best protein\n within a given LC-MS/MS data file\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protein_spectral_count\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n protein_sum_masic_abundance:\n name: protein_sum_masic_abundance\n description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n associated with the best protein from a given LC-MS/MS data file using the MASIC\n tool\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protein_sum_masic_abundance\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ProteinQuantification\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ProteinQuantification\n\nURI: nmdc:Protocol
classDiagram\n class Protocol\n click Protocol href \"../Protocol\"\n\n Protocol : name\n\n Protocol : type\n\n Protocol : url\n\n\n\nname: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- url\n- name\n- type\nclass_uri: nmdc:Protocol\n\nname: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: url\n owner: Protocol\n domain_of:\n - ImageValue\n - Protocol\n - DataObject\n range: string\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Protocol\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Protocol\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Protocol\n\nThe possible protocols that may be followed for an assay.
URI: ProtocolCategoryEnum
"},{"location":"ProtocolCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mplex None derivatization None filter_clean_up None organic_matter_extraction None solid_phase_extraction None phosphorus_extraction None ph_measurement None respiration_measurement None texture_measurement None dna_extraction None phenol_chloroform_extraction None"},{"location":"ProtocolCategoryEnum/#slots","title":"Slots","text":"Name Description protocol_execution_category"},{"location":"ProtocolCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProtocolCategoryEnum/#schema-source","title":"Schema Source","text":"name: ProtocolCategoryEnum\ndescription: The possible protocols that may be followed for an assay.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n mplex:\n text: mplex\n derivatization:\n text: derivatization\n filter_clean_up:\n text: filter_clean_up\n organic_matter_extraction:\n text: organic_matter_extraction\n solid_phase_extraction:\n text: solid_phase_extraction\n phosphorus_extraction:\n text: phosphorus_extraction\n ph_measurement:\n text: ph_measurement\n respiration_measurement:\n text: respiration_measurement\n texture_measurement:\n text: texture_measurement\n dna_extraction:\n text: dna_extraction\n phenol_chloroform_extraction:\n text: phenol_chloroform_extraction\n\nA PlannedProces that has PlannedProcess parts. Can be used to represent the case of someone following a Protocol.
URI: nmdc:ProtocolExecution
classDiagram\n class ProtocolExecution\n click ProtocolExecution href \"../ProtocolExecution\"\n PlannedProcess <|-- ProtocolExecution\n click PlannedProcess href \"../PlannedProcess\"\n\n\n\n ProtocolExecution : alternative_identifiers\n\n ProtocolExecution : description\n\n ProtocolExecution : end_date\n\n ProtocolExecution : has_failure_categorization\n\n ProtocolExecution --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ProtocolExecution : has_input\n\n ProtocolExecution --> \"*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n ProtocolExecution : has_output\n\n ProtocolExecution --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n ProtocolExecution : has_process_parts\n\n ProtocolExecution --> \"1..*\" PlannedProcess : has_process_parts\n click PlannedProcess href \"../PlannedProcess\"\n\n ProtocolExecution : id\n\n ProtocolExecution : name\n\n ProtocolExecution : processing_institution\n\n ProtocolExecution --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ProtocolExecution : protocol_execution_category\n\n ProtocolExecution --> \"1\" ProtocolCategoryEnum : protocol_execution_category\n click ProtocolCategoryEnum href \"../ProtocolCategoryEnum\"\n\n ProtocolExecution : protocol_link\n\n ProtocolExecution --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ProtocolExecution : qc_comment\n\n ProtocolExecution : qc_status\n\n ProtocolExecution --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ProtocolExecution : start_date\n\n ProtocolExecution : type\n\n\n\nname: ProtocolExecution\ndescription: A PlannedProces that has PlannedProcess parts. Can be used to represent\n the case of someone following a Protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: PlannedProcess\nslots:\n- has_process_parts\n- protocol_execution_category\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_process_parts:\n name: has_process_parts\n description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ProtocolExecution\n\nname: ProtocolExecution\ndescription: A PlannedProces that has PlannedProcess parts. Can be used to represent\n the case of someone following a Protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: PlannedProcess\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_process_parts:\n name: has_process_parts\n description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n has_process_parts:\n name: has_process_parts\n description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n list_elements_ordered: true\n alias: has_process_parts\n owner: ProtocolExecution\n domain_of:\n - ProtocolExecution\n range: PlannedProcess\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n interpolated: true\n protocol_execution_category:\n name: protocol_execution_category\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_execution_category\n owner: ProtocolExecution\n domain_of:\n - ProtocolExecution\n range: ProtocolCategoryEnum\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ProtocolExecution\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ProtocolExecution\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ProtocolExecution\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ProtocolExecution\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ProtocolExecution\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ProtocolExecution\n\nURI: QuadPosEnum
"},{"location":"QuadPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description North side None West side None South side None East side None"},{"location":"QuadPosEnum/#slots","title":"Slots","text":"Name Description quad_pos The quadrant position of the sampling room within the building"},{"location":"QuadPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"QuadPosEnum/#schema-source","title":"Schema Source","text":"name: quad_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n North side:\n text: North side\n West side:\n text: West side\n South side:\n text: South side\n East side:\n text: East side\n\nA simple quantity, e.g. 2cm
URI: nmdc:QuantityValue
classDiagram\n class QuantityValue\n click QuantityValue href \"../QuantityValue\"\n AttributeValue <|-- QuantityValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n QuantityValue : has_maximum_numeric_value\n\n QuantityValue : has_minimum_numeric_value\n\n QuantityValue : has_numeric_value\n\n QuantityValue : has_raw_value\n\n QuantityValue : has_unit\n\n QuantityValue : type\n\n\n\nname: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslots:\n- has_maximum_numeric_value\n- has_minimum_numeric_value\n- has_numeric_value\n- has_unit\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n has_unit:\n name: has_unit\n description: The unit of the quantity\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\nclass_uri: nmdc:QuantityValue\n\nname: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n has_unit:\n name: has_unit\n description: The unit of the quantity\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\nattributes:\n has_maximum_numeric_value:\n name: has_maximum_numeric_value\n description: The maximum value part, expressed as number, of the quantity value\n when the value covers a range.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_numeric_value\n alias: has_maximum_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: decimal\n has_minimum_numeric_value:\n name: has_minimum_numeric_value\n description: The minimum value part, expressed as number, of the quantity value\n when the value covers a range.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_numeric_value\n alias: has_minimum_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: decimal\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - qud:quantityValue\n - schema:value\n rank: 1000\n alias: has_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: decimal\n has_unit:\n name: has_unit\n description: The unit of the quantity\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - scale\n mappings:\n - qud:unit\n - schema:unitCode\n rank: 1000\n alias: has_unit\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: unit\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: QuantityValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: QuantityValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:QuantityValue\n\nURI: RNASampleFormatEnum
"},{"location":"RNASampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"RNASampleFormatEnum/#slots","title":"Slots","text":"Name Description rna_sample_format Solution in which the RNA sample has been suspended"},{"location":"RNASampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RNASampleFormatEnum/#schema-source","title":"Schema Source","text":"name: RNASampleFormatEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 10 mM Tris-HCl:\n text: 10 mM Tris-HCl\n DNAStable:\n text: DNAStable\n Ethanol:\n text: Ethanol\n Low EDTA TE:\n text: Low EDTA TE\n MDA reaction buffer:\n text: MDA reaction buffer\n PBS:\n text: PBS\n Pellet:\n text: Pellet\n RNAStable:\n text: RNAStable\n TE:\n text: TE\n Water:\n text: Water\n Gentegra-DNA:\n text: Gentegra-DNA\n Gentegra-RNA:\n text: Gentegra-RNA\n\nA workflow execution activity that performs taxonomy classification using sequencing reads
URI: nmdc:ReadBasedTaxonomyAnalysis
classDiagram\n class ReadBasedTaxonomyAnalysis\n click ReadBasedTaxonomyAnalysis href \"../ReadBasedTaxonomyAnalysis\"\n WorkflowExecution <|-- ReadBasedTaxonomyAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n ReadBasedTaxonomyAnalysis : alternative_identifiers\n\n ReadBasedTaxonomyAnalysis : description\n\n ReadBasedTaxonomyAnalysis : end_date\n\n ReadBasedTaxonomyAnalysis : ended_at_time\n\n ReadBasedTaxonomyAnalysis : execution_resource\n\n ReadBasedTaxonomyAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n ReadBasedTaxonomyAnalysis : git_url\n\n ReadBasedTaxonomyAnalysis : has_failure_categorization\n\n ReadBasedTaxonomyAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ReadBasedTaxonomyAnalysis : has_input\n\n ReadBasedTaxonomyAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n ReadBasedTaxonomyAnalysis : has_output\n\n ReadBasedTaxonomyAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n ReadBasedTaxonomyAnalysis : id\n\n ReadBasedTaxonomyAnalysis : name\n\n ReadBasedTaxonomyAnalysis : processing_institution\n\n ReadBasedTaxonomyAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ReadBasedTaxonomyAnalysis : protocol_link\n\n ReadBasedTaxonomyAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ReadBasedTaxonomyAnalysis : qc_comment\n\n ReadBasedTaxonomyAnalysis : qc_status\n\n ReadBasedTaxonomyAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ReadBasedTaxonomyAnalysis : start_date\n\n ReadBasedTaxonomyAnalysis : started_at_time\n\n ReadBasedTaxonomyAnalysis : type\n\n ReadBasedTaxonomyAnalysis : version\n\n ReadBasedTaxonomyAnalysis : was_informed_by\n\n ReadBasedTaxonomyAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: ReadBasedTaxonomyAnalysis\ndescription: A workflow execution activity that performs taxonomy classification using\n sequencing reads\ntitle: Read based analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ReadBasedTaxonomyAnalysis\n\nname: ReadBasedTaxonomyAnalysis\ndescription: A workflow execution activity that performs taxonomy classification using\n sequencing reads\ntitle: Read based analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ReadBasedTaxonomyAnalysis\n\nA workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
URI: nmdc:ReadQcAnalysis
classDiagram\n class ReadQcAnalysis\n click ReadQcAnalysis href \"../ReadQcAnalysis\"\n WorkflowExecution <|-- ReadQcAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n ReadQcAnalysis : alternative_identifiers\n\n ReadQcAnalysis : description\n\n ReadQcAnalysis : end_date\n\n ReadQcAnalysis : ended_at_time\n\n ReadQcAnalysis : execution_resource\n\n ReadQcAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n ReadQcAnalysis : git_url\n\n ReadQcAnalysis : has_failure_categorization\n\n ReadQcAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ReadQcAnalysis : has_input\n\n ReadQcAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n ReadQcAnalysis : has_output\n\n ReadQcAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n ReadQcAnalysis : id\n\n ReadQcAnalysis : input_base_count\n\n ReadQcAnalysis : input_read_bases\n\n ReadQcAnalysis : input_read_count\n\n ReadQcAnalysis : name\n\n ReadQcAnalysis : output_base_count\n\n ReadQcAnalysis : output_read_bases\n\n ReadQcAnalysis : output_read_count\n\n ReadQcAnalysis : processing_institution\n\n ReadQcAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ReadQcAnalysis : protocol_link\n\n ReadQcAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ReadQcAnalysis : qc_comment\n\n ReadQcAnalysis : qc_status\n\n ReadQcAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ReadQcAnalysis : start_date\n\n ReadQcAnalysis : started_at_time\n\n ReadQcAnalysis : type\n\n ReadQcAnalysis : version\n\n ReadQcAnalysis : was_informed_by\n\n ReadQcAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: ReadQcAnalysis\ndescription: A workflow execution activity that performs quality control on raw Illumina\n reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- input_base_count\n- input_read_bases\n- input_read_count\n- output_base_count\n- output_read_bases\n- output_read_count\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ReadQcAnalysis\n\nname: ReadQcAnalysis\ndescription: A workflow execution activity that performs quality control on raw Illumina\n reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n input_base_count:\n name: input_base_count\n description: The nucleotide base count number of input reads for QC analysis.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: input_base_count\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n input_read_bases:\n name: input_read_bases\n description: 'TODO '\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: input_read_bases\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n input_read_count:\n name: input_read_count\n description: The sequence count number of input reads for QC analysis.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: input_read_count\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n output_base_count:\n name: output_base_count\n description: After QC analysis nucleotide base count number.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: output_base_count\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n output_read_bases:\n name: output_read_bases\n description: TODO\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: output_read_bases\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n output_read_count:\n name: output_read_count\n description: After QC analysis sequence count number.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: output_read_count\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ReadQcAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ReadQcAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ReadQcAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ReadQcAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ReadQcAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ReadQcAnalysis\n\nURI: RelSampLocEnum
"},{"location":"RelSampLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description edge of car None center of car None under a seat None"},{"location":"RelSampLocEnum/#slots","title":"Slots","text":"Name Description rel_samp_loc The sampling location within the train car"},{"location":"RelSampLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RelSampLocEnum/#schema-source","title":"Schema Source","text":"name: rel_samp_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n edge of car:\n text: edge of car\n center of car:\n text: center of car\n under a seat:\n text: under a seat\n\nURI: ResolutionCategoryEnum
"},{"location":"ResolutionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description high None higher than unit resolution low None at unit resolution"},{"location":"ResolutionCategoryEnum/#slots","title":"Slots","text":"Name Description resolution_categories The relative resolution at which spectra were collected"},{"location":"ResolutionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ResolutionCategoryEnum/#schema-source","title":"Schema Source","text":"name: ResolutionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n high:\n text: high\n description: higher than unit resolution\n low:\n text: low\n description: at unit resolution\n\nURI: RoomCondtEnum
"},{"location":"RoomCondtEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None visible signs of mold/mildew None"},{"location":"RoomCondtEnum/#slots","title":"Slots","text":"Name Description room_condt The condition of the room at the time of sampling"},{"location":"RoomCondtEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomCondtEnum/#schema-source","title":"Schema Source","text":"name: room_condt_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n visible signs of mold/mildew:\n text: visible signs of mold/mildew\n\nURI: RoomConnectedEnum
"},{"location":"RoomConnectedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None office None stairwell None"},{"location":"RoomConnectedEnum/#slots","title":"Slots","text":"Name Description room_connected List of rooms connected to the sampling room by a doorway"},{"location":"RoomConnectedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomConnectedEnum/#schema-source","title":"Schema Source","text":"name: room_connected_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n attic:\n text: attic\n bathroom:\n text: bathroom\n closet:\n text: closet\n conference room:\n text: conference room\n elevator:\n text: elevator\n examining room:\n text: examining room\n hallway:\n text: hallway\n kitchen:\n text: kitchen\n mail room:\n text: mail room\n office:\n text: office\n stairwell:\n text: stairwell\n\nURI: RoomLocEnum
"},{"location":"RoomLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description corner room None interior room None exterior wall None"},{"location":"RoomLocEnum/#slots","title":"Slots","text":"Name Description room_loc The position of the room within the building"},{"location":"RoomLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomLocEnum/#schema-source","title":"Schema Source","text":"name: room_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n corner room:\n text: corner room\n interior room:\n text: interior room\n exterior wall:\n text: exterior wall\n\nURI: RoomSampPosEnum
"},{"location":"RoomSampPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north corner None south corner None west corner None east corner None northeast corner None northwest corner None southeast corner None southwest corner None center None"},{"location":"RoomSampPosEnum/#slots","title":"Slots","text":"Name Description room_samp_pos The horizontal sampling position in the room relative to architectural elemen..."},{"location":"RoomSampPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomSampPosEnum/#schema-source","title":"Schema Source","text":"name: room_samp_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north corner:\n text: north corner\n south corner:\n text: south corner\n west corner:\n text: west corner\n east corner:\n text: east corner\n northeast corner:\n text: northeast corner\n northwest corner:\n text: northwest corner\n southeast corner:\n text: southeast corner\n southwest corner:\n text: southwest corner\n center:\n text: center\n\nURI: RoomTypeEnum
"},{"location":"RoomTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None private office None open office None stairwell None ,restroom None lobby None vestibule None mechanical or electrical room None data center None laboratory_wet None laboratory_dry None gymnasium None natatorium None auditorium None lockers None cafe None warehouse None"},{"location":"RoomTypeEnum/#slots","title":"Slots","text":"Name Description room_type The main purpose or activity of the sampling room"},{"location":"RoomTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomTypeEnum/#schema-source","title":"Schema Source","text":"name: room_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n attic:\n text: attic\n bathroom:\n text: bathroom\n closet:\n text: closet\n conference room:\n text: conference room\n elevator:\n text: elevator\n examining room:\n text: examining room\n hallway:\n text: hallway\n kitchen:\n text: kitchen\n mail room:\n text: mail room\n private office:\n text: private office\n open office:\n text: open office\n stairwell:\n text: stairwell\n ',restroom':\n text: ',restroom'\n lobby:\n text: lobby\n vestibule:\n text: vestibule\n mechanical or electrical room:\n text: mechanical or electrical room\n data center:\n text: data center\n laboratory_wet:\n text: laboratory_wet\n laboratory_dry:\n text: laboratory_dry\n gymnasium:\n text: gymnasium\n natatorium:\n text: natatorium\n auditorium:\n text: auditorium\n lockers:\n text: lockers\n cafe:\n text: cafe\n warehouse:\n text: warehouse\n\nURI: SampCaptStatusEnum
"},{"location":"SampCaptStatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description active surveillance in response to an outbreak None active surveillance not initiated by an outbreak None farm sample None market sample None other None"},{"location":"SampCaptStatusEnum/#slots","title":"Slots","text":"Name Description samp_capt_status Reason for the sample"},{"location":"SampCaptStatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCaptStatusEnum/#schema-source","title":"Schema Source","text":"name: samp_capt_status_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n active surveillance in response to an outbreak:\n text: active surveillance in response to an outbreak\n active surveillance not initiated by an outbreak:\n text: active surveillance not initiated by an outbreak\n farm sample:\n text: farm sample\n market sample:\n text: market sample\n other:\n text: other\n\nURI: SampCollectPointEnum
"},{"location":"SampCollectPointEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description well None test well None drilling rig None wellhead None separator None storage tank None other None"},{"location":"SampCollectPointEnum/#slots","title":"Slots","text":"Name Description samp_collect_point Sampling point on the asset were sample was collected (e"},{"location":"SampCollectPointEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCollectPointEnum/#schema-source","title":"Schema Source","text":"name: samp_collect_point_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n well:\n text: well\n test well:\n text: test well\n drilling rig:\n text: drilling rig\n wellhead:\n text: wellhead\n separator:\n text: separator\n storage tank:\n text: storage tank\n other:\n text: other\n\nURI: SampDisStageEnum
"},{"location":"SampDisStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dissemination None growth and reproduction None infection None inoculation None penetration None other None"},{"location":"SampDisStageEnum/#slots","title":"Slots","text":"Name Description samp_dis_stage Stage of the disease at the time of sample collection, e"},{"location":"SampDisStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampDisStageEnum/#schema-source","title":"Schema Source","text":"name: samp_dis_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n dissemination:\n text: dissemination\n growth and reproduction:\n text: growth and reproduction\n infection:\n text: infection\n inoculation:\n text: inoculation\n penetration:\n text: penetration\n other:\n text: other\n\nURI: SampFloorEnum
"},{"location":"SampFloorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 1st floor None 2nd floor None basement None lobby None"},{"location":"SampFloorEnum/#slots","title":"Slots","text":"Name Description samp_floor The floor of the building, where the sampling room is located"},{"location":"SampFloorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampFloorEnum/#schema-source","title":"Schema Source","text":"name: samp_floor_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 1st floor:\n text: 1st floor\n 2nd floor:\n text: 2nd floor\n basement:\n text: basement\n lobby:\n text: lobby\n\nURI: SampMdEnum
"},{"location":"SampMdEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DF None RT None KB None MSL None other None"},{"location":"SampMdEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampMdEnum/#schema-source","title":"Schema Source","text":"name: samp_md_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DF:\n text: DF\n RT:\n text: RT\n KB:\n text: KB\n MSL:\n text: MSL\n other:\n text: other\n\nURI: SampSubtypeEnum
"},{"location":"SampSubtypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description oil phase None water phase None biofilm None not applicable None other None"},{"location":"SampSubtypeEnum/#slots","title":"Slots","text":"Name Description samp_subtype Name of sample sub-type"},{"location":"SampSubtypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampSubtypeEnum/#schema-source","title":"Schema Source","text":"name: samp_subtype_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n oil phase:\n text: oil phase\n water phase:\n text: water phase\n biofilm:\n text: biofilm\n not applicable:\n text: not applicable\n other:\n text: other\n\nURI: SampWeatherEnum
"},{"location":"SampWeatherEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clear sky None cloudy None foggy None hail None rain None snow None sleet None sunny None windy None"},{"location":"SampWeatherEnum/#slots","title":"Slots","text":"Name Description samp_weather The weather on the sampling day"},{"location":"SampWeatherEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampWeatherEnum/#schema-source","title":"Schema Source","text":"name: samp_weather_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n clear sky:\n text: clear sky\n cloudy:\n text: cloudy\n foggy:\n text: foggy\n hail:\n text: hail\n rain:\n text: rain\n snow:\n text: snow\n sleet:\n text: sleet\n sunny:\n text: sunny\n windy:\n text: windy\n\nA sample is a material entity that can be characterized by an experiment.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:Sample
classDiagram\n class Sample\n click Sample href \"../Sample\"\n MaterialEntity <|-- Sample\n click MaterialEntity href \"../MaterialEntity\"\n\n\n Sample <|-- Biosample\n click Biosample href \"../Biosample\"\n Sample <|-- ProcessedSample\n click ProcessedSample href \"../ProcessedSample\"\n\n\n\n Sample : alternative_identifiers\n\n Sample : description\n\n Sample : id\n\n Sample : name\n\n Sample : type\n\n\n\nname: Sample\ndescription: A sample is a material entity that can be characterized by an experiment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nclass_uri: nmdc:Sample\n\nname: Sample\ndescription: A sample is a material entity that can be characterized by an experiment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Sample\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Sample\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Sample\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Sample\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Sample\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Sample\n\nURI: SamplePortionEnum
"},{"location":"SamplePortionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description supernatant None pellet None organic_layer None aqueous_layer None non_polar_layer None"},{"location":"SamplePortionEnum/#slots","title":"Slots","text":"Name Description sampled_portion The portion of the sample that is taken for downstream activity"},{"location":"SamplePortionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SamplePortionEnum/#schema-source","title":"Schema Source","text":"name: SamplePortionEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n supernatant:\n text: supernatant\n aliases:\n - top_layer\n pellet:\n text: pellet\n aliases:\n - bottom_layer\n organic_layer:\n text: organic_layer\n aqueous_layer:\n text: aqueous_layer\n non_polar_layer:\n text: non_polar_layer\n\nURI: SampleStateEnum
"},{"location":"SampleStateEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description solid None liquid None gas None"},{"location":"SampleStateEnum/#slots","title":"Slots","text":"Name Description sample_state_information The chemical phase of a pure sample, or the state of a mixed sample"},{"location":"SampleStateEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleStateEnum/#schema-source","title":"Schema Source","text":"name: SampleStateEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n solid:\n text: solid\n liquid:\n text: liquid\n gas:\n text: gas\n\nURI: SampleTypeEnum
"},{"location":"SampleTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description soil None soil - water extract None plant associated None sediment None water None"},{"location":"SampleTypeEnum/#slots","title":"Slots","text":"Name Description sample_type Type of sample being submitted"},{"location":"SampleTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleTypeEnum/#schema-source","title":"Schema Source","text":"name: SampleTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n soil:\n text: soil\n soil - water extract:\n text: soil - water extract\n plant associated:\n text: plant associated\n sediment:\n text: sediment\n water:\n text: water\n\nURI: SeasonUseEnum
"},{"location":"SeasonUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Spring None Summer None Fall None Winter None"},{"location":"SeasonUseEnum/#slots","title":"Slots","text":"Name Description season_use The seasons the space is occupied"},{"location":"SeasonUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeasonUseEnum/#schema-source","title":"Schema Source","text":"name: season_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Spring:\n text: Spring\n Summer:\n text: Summer\n Fall:\n text: Fall\n Winter:\n text: Winter\n\nURI: SedimentTypeEnum
"},{"location":"SedimentTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description biogenous None cosmogenous None hydrogenous None lithogenous None"},{"location":"SedimentTypeEnum/#slots","title":"Slots","text":"Name Description sediment_type Information about the sediment type based on major constituents"},{"location":"SedimentTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SedimentTypeEnum/#schema-source","title":"Schema Source","text":"name: sediment_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n biogenous:\n text: biogenous\n cosmogenous:\n text: cosmogenous\n hydrogenous:\n text: hydrogenous\n lithogenous:\n text: lithogenous\n\nThe tool/substance used to separate or filter a solution or mixture.
URI: SeparationMethodEnum
"},{"location":"SeparationMethodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ptfe_96_well_filter_plate None syringe None"},{"location":"SeparationMethodEnum/#slots","title":"Slots","text":"Name Description separation_method The method that was used to separate a substance from a solution or mixture"},{"location":"SeparationMethodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeparationMethodEnum/#schema-source","title":"Schema Source","text":"name: SeparationMethodEnum\ndescription: The tool/substance used to separate or filter a solution or mixture.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\npermissible_values:\n ptfe_96_well_filter_plate:\n text: ptfe_96_well_filter_plate\n syringe:\n text: syringe\n\nURI: ShadingDeviceCondEnum
"},{"location":"ShadingDeviceCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"ShadingDeviceCondEnum/#slots","title":"Slots","text":"Name Description shading_device_cond The physical condition of the shading device at the time of sampling"},{"location":"ShadingDeviceCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceCondEnum/#schema-source","title":"Schema Source","text":"name: shading_device_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: ShadingDeviceTypeEnum
"},{"location":"ShadingDeviceTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bahama shutters None exterior roll blind None gambrel awning None hood awning None porchroller awning None sarasota shutters None slatted aluminum None solid aluminum awning None sun screen None tree None trellis None venetian awning None"},{"location":"ShadingDeviceTypeEnum/#slots","title":"Slots","text":"Name Description shading_device_type The type of shading device"},{"location":"ShadingDeviceTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceTypeEnum/#schema-source","title":"Schema Source","text":"name: shading_device_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bahama shutters:\n text: bahama shutters\n exterior roll blind:\n text: exterior roll blind\n gambrel awning:\n text: gambrel awning\n hood awning:\n text: hood awning\n porchroller awning:\n text: porchroller awning\n sarasota shutters:\n text: sarasota shutters\n slatted aluminum:\n text: slatted aluminum\n solid aluminum awning:\n text: solid aluminum awning\n sun screen:\n text: sun screen\n tree:\n text: tree\n trellis:\n text: trellis\n venetian awning:\n text: venetian awning\n\nNote
This is an abstract class and should not be instantiated directly.
URI: nmdc:Site
classDiagram\n class Site\n click Site href \"../Site\"\n MaterialEntity <|-- Site\n click MaterialEntity href \"../MaterialEntity\"\n\n\n Site <|-- FieldResearchSite\n click FieldResearchSite href \"../FieldResearchSite\"\n\n\n\n Site : alternative_identifiers\n\n Site : description\n\n Site : id\n\n Site : name\n\n Site : type\n\n\n\nname: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nclass_uri: nmdc:Site\n\nname: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Site\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Site\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Site\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Site\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Site\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Site\n\nURI: SoilHorizonEnum
"},{"location":"SoilHorizonEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description O horizon None A horizon None E horizon None B horizon None C horizon None R layer None Permafrost None M horizon None"},{"location":"SoilHorizonEnum/#slots","title":"Slots","text":"Name Description soil_horizon Specific layer in the land area which measures parallel to the soil surface a..."},{"location":"SoilHorizonEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SoilHorizonEnum/#schema-source","title":"Schema Source","text":"name: soil_horizon_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n O horizon:\n text: O horizon\n A horizon:\n text: A horizon\n E horizon:\n text: E horizon\n B horizon:\n text: B horizon\n C horizon:\n text: C horizon\n R layer:\n text: R layer\n Permafrost:\n text: Permafrost\n M horizon:\n text: M horizon\n\nA string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
URI: xsd:string
base: str
uri: xsd:string
repr: str
URI: SpecificEnum
"},{"location":"SpecificEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None photos None"},{"location":"SpecificEnum/#slots","title":"Slots","text":"Name Description specific The building specifications"},{"location":"SpecificEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SpecificEnum/#schema-source","title":"Schema Source","text":"name: specific_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n operation:\n text: operation\n as built:\n text: as built\n construction:\n text: construction\n bid:\n text: bid\n design:\n text: design\n photos:\n text: photos\n\nURI: SrDepEnvEnum
"},{"location":"SrDepEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Lacustine None Fluvioldeltaic None Fluviomarine None Marine None other None"},{"location":"SrDepEnvEnum/#slots","title":"Slots","text":"Name Description sr_dep_env Source rock depositional environment (https://en"},{"location":"SrDepEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrDepEnvEnum/#schema-source","title":"Schema Source","text":"name: sr_dep_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Lacustine:\n text: Lacustine\n Fluvioldeltaic:\n text: Fluvioldeltaic\n Fluviomarine:\n text: Fluviomarine\n Marine:\n text: Marine\n other:\n text: other\n\nURI: SrGeolAgeEnum
"},{"location":"SrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"SrGeolAgeEnum/#slots","title":"Slots","text":"Name Description sr_geol_age Geological age of source rock (Additional info: https://en"},{"location":"SrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrGeolAgeEnum/#schema-source","title":"Schema Source","text":"name: sr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Archean:\n text: Archean\n Cambrian:\n text: Cambrian\n Carboniferous:\n text: Carboniferous\n Cenozoic:\n text: Cenozoic\n Cretaceous:\n text: Cretaceous\n Devonian:\n text: Devonian\n Jurassic:\n text: Jurassic\n Mesozoic:\n text: Mesozoic\n Neogene:\n text: Neogene\n Ordovician:\n text: Ordovician\n Paleogene:\n text: Paleogene\n Paleozoic:\n text: Paleozoic\n Permian:\n text: Permian\n Precambrian:\n text: Precambrian\n Proterozoic:\n text: Proterozoic\n Silurian:\n text: Silurian\n Triassic:\n text: Triassic\n other:\n text: other\n\nURI: SrKerogTypeEnum
"},{"location":"SrKerogTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Type I None Type II None Type III None Type IV None other None"},{"location":"SrKerogTypeEnum/#slots","title":"Slots","text":"Name Description sr_kerog_type Origin of kerogen"},{"location":"SrKerogTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrKerogTypeEnum/#schema-source","title":"Schema Source","text":"name: sr_kerog_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Type I:\n text: Type I\n Type II:\n text: Type II\n Type III:\n text: Type III\n Type IV:\n text: Type IV\n other:\n text: other\n\nURI: SrLithologyEnum
"},{"location":"SrLithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Clastic None Carbonate None Coal None Biosilicieous None other None"},{"location":"SrLithologyEnum/#slots","title":"Slots","text":"Name Description sr_lithology Lithology of source rock (https://en"},{"location":"SrLithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrLithologyEnum/#schema-source","title":"Schema Source","text":"name: sr_lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Clastic:\n text: Clastic\n Carbonate:\n text: Carbonate\n Coal:\n text: Coal\n Biosilicieous:\n text: Biosilicieous\n other:\n text: other\n\nThe type of stationary phase used in a chromatography process.
URI: StationaryPhaseEnum
"},{"location":"StationaryPhaseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description BEH-HILIC None C18 None C8 None C4 None C2 None C1 None C30 None C60 None CNT None CN None Diol None HILIC None NH2 None Phenyl None Polysiloxane None PS-DVB None SAX None SCX None Silica None WCX None WAX None ZIC-HILIC None ZIC-pHILIC None ZIC-cHILIC None"},{"location":"StationaryPhaseEnum/#slots","title":"Slots","text":"Name Description stationary_phase The material the stationary phase is comprised of used in chromatography"},{"location":"StationaryPhaseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StationaryPhaseEnum/#schema-source","title":"Schema Source","text":"name: StationaryPhaseEnum\ndescription: The type of stationary phase used in a chromatography process.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-4504-1039\nrank: 1000\npermissible_values:\n BEH-HILIC:\n text: BEH-HILIC\n C18:\n text: C18\n C8:\n text: C8\n C4:\n text: C4\n C2:\n text: C2\n C1:\n text: C1\n C30:\n text: C30\n C60:\n text: C60\n CNT:\n text: CNT\n CN:\n text: CN\n Diol:\n text: Diol\n HILIC:\n text: HILIC\n NH2:\n text: NH2\n Phenyl:\n text: Phenyl\n Polysiloxane:\n text: Polysiloxane\n PS-DVB:\n text: PS-DVB\n SAX:\n text: SAX\n SCX:\n text: SCX\n Silica:\n text: Silica\n WCX:\n text: WCX\n WAX:\n text: WAX\n ZIC-HILIC:\n text: ZIC-HILIC\n ZIC-pHILIC:\n text: ZIC-pHILIC\n ZIC-cHILIC:\n text: ZIC-cHILIC\n\nURI: StatusEnum
"},{"location":"StatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description pass None fail None"},{"location":"StatusEnum/#slots","title":"Slots","text":"Name Description qc_status Stores information about the result of a process (ie the process of sequencin..."},{"location":"StatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StatusEnum/#schema-source","title":"Schema Source","text":"name: StatusEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n pass:\n text: pass\n fail:\n text: fail\n\nA planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment.
URI: nmdc:StorageProcess
classDiagram\n class StorageProcess\n click StorageProcess href \"../StorageProcess\"\n PlannedProcess <|-- StorageProcess\n click PlannedProcess href \"../PlannedProcess\"\n\n\n\n StorageProcess : alternative_identifiers\n\n StorageProcess : contained_in\n\n StorageProcess --> \"0..1\" ContainerCategoryEnum : contained_in\n click ContainerCategoryEnum href \"../ContainerCategoryEnum\"\n\n StorageProcess : description\n\n StorageProcess : end_date\n\n StorageProcess : has_failure_categorization\n\n StorageProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n StorageProcess : has_input\n\n StorageProcess --> \"*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n StorageProcess : has_output\n\n StorageProcess --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n StorageProcess : id\n\n StorageProcess : name\n\n StorageProcess : processing_institution\n\n StorageProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n StorageProcess : protocol_link\n\n StorageProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n StorageProcess : qc_comment\n\n StorageProcess : qc_status\n\n StorageProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n StorageProcess : start_date\n\n StorageProcess : substances_used\n\n StorageProcess --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n StorageProcess : temperature\n\n StorageProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n StorageProcess : type\n\n\n\nname: StorageProcess\ndescription: A planned process with the objective to preserve and protect material\n entities by placing them in an identified location which may have a controlled\n environment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0302893\nis_a: PlannedProcess\nslots:\n- substances_used\n- contained_in\n- temperature\nslot_usage:\n substances_used:\n name: substances_used\n description: The substance(s) that a processed sample is stored in.\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:StorageProcess\n\nname: StorageProcess\ndescription: A planned process with the objective to preserve and protect material\n entities by placing them in an identified location which may have a controlled\n environment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0302893\nis_a: PlannedProcess\nslot_usage:\n substances_used:\n name: substances_used\n description: The substance(s) that a processed sample is stored in.\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n substances_used:\n name: substances_used\n description: The substance(s) that a processed sample is stored in.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: StorageProcess\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n contained_in:\n name: contained_in\n description: A type of container.\n examples:\n - value: test tube\n - value: falcon tube\n - value: whirlpak\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contained_in\n owner: StorageProcess\n domain_of:\n - SubSamplingProcess\n - StorageProcess\n range: ContainerCategoryEnum\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: StorageProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: StorageProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: StorageProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: StorageProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: StorageProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: StorageProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:StorageProcess\n\nThis enumeration specifies information about stranded RNA library preparations.
URI: StrandedOrientationEnum
"},{"location":"StrandedOrientationEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description antisense orientation None Orientation that is complementary (non-coding) to a sequence of messenger RNA sense orientation None Orientation that corresponds to the coding sequence of messenger RNA"},{"location":"StrandedOrientationEnum/#slots","title":"Slots","text":"Name Description stranded_orientation Lists the strand orientiation for a stranded RNA library preparation"},{"location":"StrandedOrientationEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StrandedOrientationEnum/#schema-source","title":"Schema Source","text":"name: StrandedOrientationEnum\ndescription: This enumeration specifies information about stranded RNA library preparations.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n antisense orientation:\n text: antisense orientation\n description: Orientation that is complementary (non-coding) to a sequence of messenger\n RNA.\n comments:\n - See https://www.genome.gov/genetics-glossary/antisense\n exact_mappings:\n - SO:0000077\n sense orientation:\n text: sense orientation\n description: Orientation that corresponds to the coding sequence of messenger\n RNA.\n\nA character string
URI: xsd:string
base: str
uri: xsd:string
A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.
URI: nmdc:Study
classDiagram\n class Study\n click Study href \"../Study\"\n NamedThing <|-- Study\n click NamedThing href \"../NamedThing\"\n\n\n\n Study : alternative_descriptions\n\n Study : alternative_identifiers\n\n Study : alternative_names\n\n Study : alternative_titles\n\n Study : associated_dois\n\n Study --> \"*\" Doi : associated_dois\n click Doi href \"../Doi\"\n\n Study : description\n\n Study : ecosystem\n\n Study : ecosystem_category\n\n Study : ecosystem_subtype\n\n Study : ecosystem_type\n\n Study : emsl_project_identifiers\n\n Study : funding_sources\n\n Study : gnps_task_identifiers\n\n Study : gold_study_identifiers\n\n Study : has_credit_associations\n\n Study --> \"*\" CreditAssociation : has_credit_associations\n click CreditAssociation href \"../CreditAssociation\"\n\n Study : homepage_website\n\n Study : id\n\n Study : insdc_bioproject_identifiers\n\n Study : jgi_portal_study_identifiers\n\n Study : mgnify_project_identifiers\n\n Study : name\n\n Study : neon_study_identifiers\n\n Study : notes\n\n Study : objective\n\n Study : part_of\n\n Study --> \"*\" Study : part_of\n click Study href \"../Study\"\n\n Study : principal_investigator\n\n Study --> \"0..1\" PersonValue : principal_investigator\n click PersonValue href \"../PersonValue\"\n\n Study : protocol_link\n\n Study --> \"*\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n Study : related_identifiers\n\n Study : specific_ecosystem\n\n Study : study_category\n\n Study --> \"1\" StudyCategoryEnum : study_category\n click StudyCategoryEnum href \"../StudyCategoryEnum\"\n\n Study : study_image\n\n Study --> \"*\" ImageValue : study_image\n click ImageValue href \"../ImageValue\"\n\n Study : title\n\n Study : type\n\n Study : websites\n\n\n\nname: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n the key objective of its underlying projects.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A study (project) groups together data submitted to the archive and\n controls its release date. A study accession is typically used when citing data\n submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research initiative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslots:\n- emsl_project_identifiers\n- gnps_task_identifiers\n- gold_study_identifiers\n- insdc_bioproject_identifiers\n- jgi_portal_study_identifiers\n- mgnify_project_identifiers\n- neon_study_identifiers\n- related_identifiers\n- alternative_descriptions\n- alternative_names\n- alternative_titles\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- specific_ecosystem\n- associated_dois\n- funding_sources\n- has_credit_associations\n- homepage_website\n- notes\n- objective\n- part_of\n- principal_investigator\n- protocol_link\n- study_category\n- study_image\n- title\n- websites\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a name for the study your samples will belong with.\n websites:\n name: websites\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n homepage_website:\n name: homepage_website\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the consortium's homepage if the study_category is a consortium.\n description:\n name: description\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n notes:\n name: notes\n annotations:\n tooltip:\n tag: tooltip\n value: Add any additional notes or comments about this study.\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n alternative_names:\n name: alternative_names\n annotations:\n tooltip:\n tag: tooltip\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n part_of:\n name: part_of\n description: Links a study or consortium to a parent (or umbrella) study or consortium.\n comments:\n - Value is the id of the umbrella study or consortium.\n range: Study\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n protocol_link:\n name: protocol_link\n multivalued: true\n inlined_as_list: true\nclass_uri: nmdc:Study\n\nname: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n the key objective of its underlying projects.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A study (project) groups together data submitted to the archive and\n controls its release date. A study accession is typically used when citing data\n submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research initiative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a name for the study your samples will belong with.\n websites:\n name: websites\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n homepage_website:\n name: homepage_website\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the consortium's homepage if the study_category is a consortium.\n description:\n name: description\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n notes:\n name: notes\n annotations:\n tooltip:\n tag: tooltip\n value: Add any additional notes or comments about this study.\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n alternative_names:\n name: alternative_names\n annotations:\n tooltip:\n tag: tooltip\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n part_of:\n name: part_of\n description: Links a study or consortium to a parent (or umbrella) study or consortium.\n comments:\n - Value is the id of the umbrella study or consortium.\n range: Study\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n protocol_link:\n name: protocol_link\n multivalued: true\n inlined_as_list: true\nattributes:\n emsl_project_identifiers:\n name: emsl_project_identifiers\n description: Identifiers that link a NMDC study to the EMSL user facility website\n hosting the project description of an EMSL user project\n title: EMSL Project Identifiers\n todos:\n - elaborate on description\n notes:\n - these identifiers are all currently 5 digits long but that could change in the\n future\n examples:\n - value: emsl.project:60141\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/927#issuecomment-1802136437\n rank: 1000\n is_a: study_identifiers\n mixins:\n - emsl_identifiers\n alias: emsl_project_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^emsl\\.project:[0-9]{5}$\n gnps_task_identifiers:\n name: gnps_task_identifiers\n description: identifiers that link a NMDC study to a web-based report about metabolomics\n analysis progress and results\n title: GNPS task identifiers\n comments:\n - this could be considered a related identifier, as the metabolomics progress\n and results aren't a study per se\n - this identifier was registered with bioregistry but not identifiers.org\n examples:\n - value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysis/\n rank: 1000\n is_a: study_identifiers\n mixins:\n - gnps_identifiers\n alias: gnps_task_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^gnps\\.task:[a-f0-9]+$\n gold_study_identifiers:\n name: gold_study_identifiers\n description: identifiers for corresponding project(s) in GOLD\n title: GOLD Study Identifiers\n comments:\n - uses the prefix GS (but possibly in a different case)\n examples:\n - value: https://bioregistry.io/gold:Gs0110115\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/studies\n rank: 1000\n is_a: study_identifiers\n mixins:\n - gold_identifiers\n alias: gold_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^gold:Gs[0-9]+$\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n comments:\n - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n one to one\n examples:\n - value: https://bioregistry.io/bioproject:PRJNA366857\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2\n metatranscriptome\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ncbi.nlm.nih.gov/bioproject/\n - https://www.ddbj.nig.ac.jp/bioproject/index-e.html\n aliases:\n - NCBI bioproject identifiers\n - DDBJ bioproject identifiers\n rank: 1000\n is_a: study_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_bioproject_identifiers\n owner: Study\n domain_of:\n - NucleotideSequencing\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n jgi_portal_study_identifiers:\n name: jgi_portal_study_identifiers\n id_prefixes:\n - jgi.proposal\n description: Identifiers that link a NMDC study to a website hosting raw and analyzed\n data for a JGI proposal. The suffix of the curie can used to query the GOLD\n API and is interoperable with an award DOI from OSTI and a GOLD study identifier.\n title: JGI Portal Study identifiers\n comments:\n - Could this could be considered a related identifier?\n - Curie suffix is the Site Award Number from an OSTI award page\n - Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD\n study identifier gold:Gs0154044\n - bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\n examples:\n - value: jgi.proposal:507130\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - jgi_portal_identifiers\n alias: jgi_portal_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^jgi.proposal:\\d+$\n mgnify_project_identifiers:\n name: mgnify_project_identifiers\n description: identifiers for corresponding project in MGnify\n examples:\n - value: https://bioregistry.io/mgnify.proj:MGYS00005757\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - mgnify_identifiers\n alias: mgnify_project_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^mgnify.proj:[A-Z]+[0-9]+$\n neon_study_identifiers:\n name: neon_study_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - neon_identifiers\n alias: neon_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n title: Related Identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: related_identifiers\n owner: Study\n domain_of:\n - Study\n range: string\n alternative_descriptions:\n name: alternative_descriptions\n description: A list of alternative descriptions for the entity. The distinction\n between description and alternative descriptions is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_descriptions\n owner: Study\n domain_of:\n - Study\n range: string\n multivalued: true\n alternative_names:\n name: alternative_names\n annotations:\n tooltip:\n tag: tooltip\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: Study\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n alternative_titles:\n name: alternative_titles\n description: A list of alternative titles for the entity. The distinction between\n title and alternative titles is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n rank: 1000\n alias: alternative_titles\n owner: Study\n domain_of:\n - Study\n range: string\n multivalued: true\n ecosystem:\n name: ecosystem\n description: An ecosystem is a combination of a physical environment (abiotic\n factors) and all the organisms (biotic factors) that interact with this environment.\n Ecosystem is in position 1/5 in a GOLD path.\n comments:\n - The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism\n or environmental sample is collected. The three broad groups under Ecosystem\n are Environmental, Host-associated, and Engineered. They represent samples collected\n from a natural environment or from another organism or from engineered environments\n like bioreactors respectively.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_category:\n name: ecosystem_category\n description: Ecosystem categories represent divisions within the ecosystem based\n on specific characteristics of the environment from where an organism or sample\n is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n comments:\n - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or\n phyla and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_category\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_subtype:\n name: ecosystem_subtype\n description: Ecosystem subtypes represent further subdivision of Ecosystem types\n into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n path.\n comments:\n - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n the Ecosystem subtype category.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_subtype\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_type:\n name: ecosystem_type\n description: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still\n broad but specific to the characteristics of a given environment. Ecosystem\n type is in position 3/5 in a GOLD path.\n comments:\n - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_type\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n specific_ecosystem:\n name: specific_ecosystem\n description: Specific ecosystems represent specific features of the environment\n like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n Specific ecosystem is in position 5/5 in a GOLD path.\n comments:\n - Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: specific_ecosystem\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n associated_dois:\n name: associated_dois\n description: A list of DOIs associated with a resource, such as a list of DOIS\n associated with a Study.\n examples:\n - value: '[{''doi'': ''doi:10.46936/intm.proj.2021.60141/60000423'', ''doi_provider'':\n ''emsl'', ''doi_category'': ''award_doi''}, {''doi'': ''doi:10.1101/2022.12.12.520098'',\n ''doi_category'': ''publication_doi''}, {''doi'': ''doi:10.48321/D1Z60Q'',\n ''doi_category'': ''data_management_plan_doi'', ''doi_provider'': ''gsc''}]'\n description: Provides a list of two DOIs; specifically, an EMSL award DOI and\n a publication DOI.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Associated DOIs\n - Associated digital object identifiers\n rank: 1000\n alias: associated_dois\n owner: Study\n domain_of:\n - Study\n range: Doi\n multivalued: true\n inlined: true\n inlined_as_list: true\n funding_sources:\n name: funding_sources\n description: A list of organizations, along with the award numbers, that underwrite\n financial support for projects of a particular type. Typically, they process\n applications and award funds to the chosen qualified applicants.\n comments:\n - Include only the name of the funding organization and the award or contract\n number.\n examples:\n - value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n - value: U.S. Department of Energy, Office of Science, Office of Biological and\n Environmental Research (BER) under contract DE-AC05-00OR2275\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - NCIT:C39409\n rank: 1000\n alias: funding_sources\n owner: Study\n domain_of:\n - Study\n range: string\n multivalued: true\n has_credit_associations:\n name: has_credit_associations\n annotations:\n tooltip:\n tag: tooltip\n value: Other researchers associated with this study.\n description: 'This slot links a study to a credit association. The credit association\n will be linked to a person value and to a CRediT Contributor Roles term. Overall\n semantics: person should get credit X for their participation in the study'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: prov:qualifiedAssociation\n alias: has_credit_associations\n owner: Study\n domain_of:\n - Study\n range: CreditAssociation\n multivalued: true\n inlined: true\n inlined_as_list: true\n homepage_website:\n name: homepage_website\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the consortium's homepage if the study_category is a consortium.\n description: The website address (URL) of an entity's homepage.\n examples:\n - value: https://www.neonscience.org/\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: websites\n alias: homepage_website\n owner: Study\n domain_of:\n - Study\n range: string\n multivalued: true\n pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n maximum_cardinality: 1\n notes:\n name: notes\n annotations:\n tooltip:\n tag: tooltip\n value: Add any additional notes or comments about this study.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: notes\n owner: Study\n domain_of:\n - Study\n range: string\n objective:\n name: objective\n description: The scientific objectives associated with the entity. It SHOULD correspond\n to scientific norms for objectives field in a structured abstract.\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - SIO:000337\n rank: 1000\n alias: objective\n owner: Study\n domain_of:\n - Study\n range: string\n part_of:\n name: part_of\n description: Links a study or consortium to a parent (or umbrella) study or consortium.\n comments:\n - Value is the id of the umbrella study or consortium.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n slot_uri: dcterms:isPartOf\n alias: part_of\n owner: Study\n domain_of:\n - FieldResearchSite\n - Study\n range: Study\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n alias: principal_investigator\n owner: Study\n domain_of:\n - Study\n - DataGeneration\n range: PersonValue\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Study\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n multivalued: true\n inlined_as_list: true\n study_category:\n name: study_category\n description: The type of research initiative\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: study_category\n owner: Study\n domain_of:\n - Study\n range: StudyCategoryEnum\n required: true\n study_image:\n name: study_image\n description: Links a study to one or more images.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: study_image\n owner: Study\n domain_of:\n - Study\n range: ImageValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n title:\n name: title\n description: A name given to the entity that differs from the name/label programmatically\n assigned to it. For example, when extracting study information for GOLD, the\n GOLD system has assigned a name/label. However, for display purposes, we may\n also wish the capture the title of the proposal that was used to fund the study.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:title\n rank: 1000\n alias: title\n owner: Study\n domain_of:\n - Study\n range: string\n websites:\n name: websites\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n description: A list of websites that are associated with the entity.\n comments:\n - DOIs should not be included as websites. Instead, use the associated_dois slot.\n - A consortium's homepage website should be included in the homepage_website slot,\n not in websites.\n - consortium is a convenience term for a Study whose study_category value is consortium\n - the website slot and its subproperties are virtually identical to the url slot,\n except that they are multivalued and url is single-valued.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:url\n rank: 1000\n alias: websites\n owner: Study\n domain_of:\n - PersonValue\n - Study\n range: string\n multivalued: true\n pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Study\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a name for the study your samples will belong with.\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Study\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Study\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Study\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Study\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Study\n\nURI: StudyCategoryEnum
"},{"location":"StudyCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description research_study None A detailed examination, analysis, or critical inspection of a hypothesis-driv... consortium None A group formed to undertake a venture that is beyond the capabilities of the ..."},{"location":"StudyCategoryEnum/#slots","title":"Slots","text":"Name Description study_category The type of research initiative"},{"location":"StudyCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StudyCategoryEnum/#schema-source","title":"Schema Source","text":"name: StudyCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n research_study:\n text: research_study\n description: A detailed examination, analysis, or critical inspection of a hypothesis-driven\n experiment.\n exact_mappings:\n - SIO:001066\n - NCIT:C63536\n - ISA:Study\n close_mappings:\n - OBI:0000355\n consortium:\n text: consortium\n description: A group formed to undertake a venture that is beyond the capabilities\n of the individual members. Each member of the consortium brings a high level\n of expertise in a specific area to ensure the successful completion of the project.\n comments:\n - A consortium has collections of data, those data do not come from a hypothesis-driven\n experiment.\n exact_mappings:\n - NCIT:C61538\n\nSeparating a sample aliquot from the starting material for downstream activity.
__
URI: nmdc:SubSamplingProcess
classDiagram\n class SubSamplingProcess\n click SubSamplingProcess href \"../SubSamplingProcess\"\n MaterialProcessing <|-- SubSamplingProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n SubSamplingProcess : alternative_identifiers\n\n SubSamplingProcess : contained_in\n\n SubSamplingProcess --> \"0..1\" ContainerCategoryEnum : contained_in\n click ContainerCategoryEnum href \"../ContainerCategoryEnum\"\n\n SubSamplingProcess : container_size\n\n SubSamplingProcess --> \"0..1\" QuantityValue : container_size\n click QuantityValue href \"../QuantityValue\"\n\n SubSamplingProcess : description\n\n SubSamplingProcess : end_date\n\n SubSamplingProcess : has_failure_categorization\n\n SubSamplingProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n SubSamplingProcess : has_input\n\n SubSamplingProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n SubSamplingProcess : has_output\n\n SubSamplingProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n SubSamplingProcess : id\n\n SubSamplingProcess : instrument_used\n\n SubSamplingProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n SubSamplingProcess : mass\n\n SubSamplingProcess --> \"0..1\" QuantityValue : mass\n click QuantityValue href \"../QuantityValue\"\n\n SubSamplingProcess : name\n\n SubSamplingProcess : processing_institution\n\n SubSamplingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n SubSamplingProcess : protocol_link\n\n SubSamplingProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n SubSamplingProcess : qc_comment\n\n SubSamplingProcess : qc_status\n\n SubSamplingProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n SubSamplingProcess : sampled_portion\n\n SubSamplingProcess --> \"*\" SamplePortionEnum : sampled_portion\n click SamplePortionEnum href \"../SamplePortionEnum\"\n\n SubSamplingProcess : start_date\n\n SubSamplingProcess : temperature\n\n SubSamplingProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n SubSamplingProcess : type\n\n SubSamplingProcess : volume\n\n SubSamplingProcess --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: SubSamplingProcess\ndescription: 'Separating a sample aliquot from the starting material for downstream\n activity.\n\n '\nnotes:\n- A subsample may be (a) a portion of the sample obtained by selection or division;\n (b) an individual unit of the lot taken as part of the sample; (c) the final unit\n of multistage sampling. The term 'subsample' is used either in the sense of a 'sample\n of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent\n from the context or is defined.\n- TODO - Montana to visit slot descriptions\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0000744\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslots:\n- container_size\n- contained_in\n- temperature\n- volume\n- mass\n- sampled_portion\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The output volume of the SubSampling Process.\n mass:\n name: mass\n description: The output mass of the SubSampling Process.\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The subsample.\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:SubSamplingProcess\n\nname: SubSamplingProcess\ndescription: 'Separating a sample aliquot from the starting material for downstream\n activity.\n\n '\nnotes:\n- A subsample may be (a) a portion of the sample obtained by selection or division;\n (b) an individual unit of the lot taken as part of the sample; (c) the final unit\n of multistage sampling. The term 'subsample' is used either in the sense of a 'sample\n of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent\n from the context or is defined.\n- TODO - Montana to visit slot descriptions\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0000744\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The output volume of the SubSampling Process.\n mass:\n name: mass\n description: The output mass of the SubSampling Process.\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The subsample.\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n container_size:\n name: container_size\n description: The volume of the container an analyte is stored in or an activity\n takes place in\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: container_size\n owner: SubSamplingProcess\n domain_of:\n - SubSamplingProcess\n - FiltrationProcess\n range: QuantityValue\n contained_in:\n name: contained_in\n description: A type of container.\n examples:\n - value: test tube\n - value: falcon tube\n - value: whirlpak\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contained_in\n owner: SubSamplingProcess\n domain_of:\n - SubSamplingProcess\n - StorageProcess\n range: ContainerCategoryEnum\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: SubSamplingProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n volume:\n name: volume\n description: The output volume of the SubSampling Process.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: SubSamplingProcess\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\n mass:\n name: mass\n description: The output mass of the SubSampling Process.\n title: mass\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - PATO:0000125\n rank: 1000\n alias: mass\n owner: SubSamplingProcess\n domain_of:\n - SubSamplingProcess\n - PortionOfSubstance\n range: QuantityValue\n sampled_portion:\n name: sampled_portion\n description: The portion of the sample that is taken for downstream activity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sampled_portion\n owner: SubSamplingProcess\n domain_of:\n - SubSamplingProcess\n range: SamplePortionEnum\n multivalued: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: SubSamplingProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The subsample.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: SubSamplingProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: SubSamplingProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: SubSamplingProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: SubSamplingProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: SubSamplingProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:SubSamplingProcess\n\nURI: SubstanceRoleEnum
"},{"location":"SubstanceRoleEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description buffer CHEBI:35225 Maintains the pH of the solution within a specific range to stabilize analyte... acid CHEBI:37527 Donates a proton or accepts an electron pair in a chemical reaction base CHEBI:22695 Accepts a proton or donates an electron pair in a chemical reaction ms_proteolytic_enzyme MS:1002986 Enzyme that catalyzes the hydrolysis of proteins and is used in mass spectrom... solvent CHEBI:46787 Dissolves the sample or reagents to facilitate reactions or extraction surfactant CHEBI:35195 Reduces surface tension and aids in the solubilization of substances derivatizing_agent None Chemically modifies analytes to improve detection or separation solubilizing_agent None"},{"location":"SubstanceRoleEnum/#slots","title":"Slots","text":"Name Description substance_role The role of a substance in a process"},{"location":"SubstanceRoleEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstanceRoleEnum/#schema-source","title":"Schema Source","text":"name: SubstanceRoleEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n buffer:\n text: buffer\n description: Maintains the pH of the solution within a specific range to stabilize\n analytes or reactions.\n meaning: CHEBI:35225\n acid:\n text: acid\n description: Donates a proton or accepts an electron pair in a chemical reaction.\n meaning: CHEBI:37527\n base:\n text: base\n description: Accepts a proton or donates an electron pair in a chemical reaction.\n meaning: CHEBI:22695\n ms_proteolytic_enzyme:\n text: ms_proteolytic_enzyme\n description: Enzyme that catalyzes the hydrolysis of proteins and is used in mass\n spectrometry based proteomics\n meaning: MS:1002986\n solvent:\n text: solvent\n description: Dissolves the sample or reagents to facilitate reactions or extraction.\n meaning: CHEBI:46787\n surfactant:\n text: surfactant\n description: Reduces surface tension and aids in the solubilization of substances.\n meaning: CHEBI:35195\n derivatizing_agent:\n text: derivatizing_agent\n description: Chemically modifies analytes to improve detection or separation.\n solubilizing_agent:\n text: solubilizing_agent\n\nURI: SubstructureTypeEnum
"},{"location":"SubstructureTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crawlspace None slab on grade None basement None"},{"location":"SubstructureTypeEnum/#slots","title":"Slots","text":"Name Description substructure_type The substructure or under building is that largely hidden section of the buil..."},{"location":"SubstructureTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstructureTypeEnum/#schema-source","title":"Schema Source","text":"name: substructure_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crawlspace:\n text: crawlspace\n slab on grade:\n text: slab on grade\n basement:\n text: basement\n\nURI: SurfAirContEnum
"},{"location":"SurfAirContEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dust None organic matter None particulate matter None volatile organic compounds None biological contaminants None radon None nutrients None biocides None"},{"location":"SurfAirContEnum/#slots","title":"Slots","text":"Name Description surf_air_cont Contaminant identified on surface"},{"location":"SurfAirContEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfAirContEnum/#schema-source","title":"Schema Source","text":"name: surf_air_cont_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n dust:\n text: dust\n organic matter:\n text: organic matter\n particulate matter:\n text: particulate matter\n volatile organic compounds:\n text: volatile organic compounds\n biological contaminants:\n text: biological contaminants\n radon:\n text: radon\n nutrients:\n text: nutrients\n biocides:\n text: biocides\n\nURI: SurfMaterialEnum
"},{"location":"SurfMaterialEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description adobe None carpet None cinder blocks None concrete None hay bales None glass None metal None paint None plastic None stainless steel None stone None stucco None tile None vinyl None wood None"},{"location":"SurfMaterialEnum/#slots","title":"Slots","text":"Name Description surf_material Surface materials at the point of sampling"},{"location":"SurfMaterialEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfMaterialEnum/#schema-source","title":"Schema Source","text":"name: surf_material_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n adobe:\n text: adobe\n carpet:\n text: carpet\n cinder blocks:\n text: cinder blocks\n concrete:\n text: concrete\n hay bales:\n text: hay bales\n glass:\n text: glass\n metal:\n text: metal\n paint:\n text: paint\n plastic:\n text: plastic\n stainless steel:\n text: stainless steel\n stone:\n text: stone\n stucco:\n text: stucco\n tile:\n text: tile\n vinyl:\n text: vinyl\n wood:\n text: wood\n\nURI: TargetGeneEnum
"},{"location":"TargetGeneEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 16S_rRNA None the small subunit of the bacterial/archean ribosome 23S_rRNA None the large subunit of the bacterial/archean ribosome 18S_rRNA None the small subunit of the eukaryotic ribosome 28S_rRNA None the large subunit of the eukaryotic ribosome"},{"location":"TargetGeneEnum/#slots","title":"Slots","text":"Name Description target_gene Targeted gene or locus name for marker gene studies"},{"location":"TargetGeneEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TargetGeneEnum/#schema-source","title":"Schema Source","text":"name: TargetGeneEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 16S_rRNA:\n text: 16S_rRNA\n description: the small subunit of the bacterial/archean ribosome\n aliases:\n - 16S rRNA\n - 16S ribosomal RNA\n narrow_mappings:\n - OBI:0002763\n 23S_rRNA:\n text: 23S_rRNA\n description: the large subunit of the bacterial/archean ribosome\n aliases:\n - 23S rRNA\n - 23S ribosomal RNA\n 18S_rRNA:\n text: 18S_rRNA\n description: the small subunit of the eukaryotic ribosome\n aliases:\n - 18S rRNA\n - 18S ribosomal RNA\n 28S_rRNA:\n text: 28S_rRNA\n description: the large subunit of the eukaryotic ribosome\n aliases:\n - -28S rRNA - 28S ribosomal RNA\n\nA basic string value
URI: nmdc:TextValue
classDiagram\n class TextValue\n click TextValue href \"../TextValue\"\n AttributeValue <|-- TextValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n TextValue : has_raw_value\n\n TextValue : language\n\n TextValue : type\n\n\n\nname: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- language\nclass_uri: nmdc:TextValue\n\nname: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n language:\n name: language\n description: Should use ISO 639-1 code e.g. \"en\", \"fr\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: language\n owner: TextValue\n domain_of:\n - TextValue\n range: language_code\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: TextValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: TextValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:TextValue\n\nURI: TidalStageEnum
"},{"location":"TidalStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low tide None ebb tide None flood tide None high tide None"},{"location":"TidalStageEnum/#slots","title":"Slots","text":"Name Description tidal_stage Stage of tide"},{"location":"TidalStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TidalStageEnum/#schema-source","title":"Schema Source","text":"name: tidal_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n low tide:\n text: low tide\n ebb tide:\n text: ebb tide\n flood tide:\n text: flood tide\n high tide:\n text: high tide\n\nURI: TillageEnum
"},{"location":"TillageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drill None cutting disc None ridge till None strip tillage None zonal tillage None chisel None tined None mouldboard None disc plough None"},{"location":"TillageEnum/#slots","title":"Slots","text":"Name Description tillage Note method(s) used for tilling"},{"location":"TillageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TillageEnum/#schema-source","title":"Schema Source","text":"name: tillage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n drill:\n text: drill\n cutting disc:\n text: cutting disc\n ridge till:\n text: ridge till\n strip tillage:\n text: strip tillage\n zonal tillage:\n text: zonal tillage\n chisel:\n text: chisel\n tined:\n text: tined\n mouldboard:\n text: mouldboard\n disc plough:\n text: disc plough\n\nA time object represents a (local) time of day, independent of any particular day
URI: xsd:time
base: XSDTime
uri: xsd:time
repr: str
A value that is a timestamp. The range should be ISO-8601
URI: nmdc:TimestampValue
classDiagram\n class TimestampValue\n click TimestampValue href \"../TimestampValue\"\n AttributeValue <|-- TimestampValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n TimestampValue : has_raw_value\n\n TimestampValue : type\n\n\n\nname: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nclass_uri: nmdc:TimestampValue\n\nname: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: TimestampValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: TimestampValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:TimestampValue\n\nURI: TrainLineEnum
"},{"location":"TrainLineEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description red None green None orange None"},{"location":"TrainLineEnum/#slots","title":"Slots","text":"Name Description train_line The subway line name"},{"location":"TrainLineEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainLineEnum/#schema-source","title":"Schema Source","text":"name: train_line_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n red:\n text: red\n green:\n text: green\n orange:\n text: orange\n\nURI: TrainStatLocEnum
"},{"location":"TrainStatLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description south station above ground None south station underground None south station amtrak None forest hills None riverside None"},{"location":"TrainStatLocEnum/#slots","title":"Slots","text":"Name Description train_stat_loc The train station collection location"},{"location":"TrainStatLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStatLocEnum/#schema-source","title":"Schema Source","text":"name: train_stat_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n south station above ground:\n text: south station above ground\n south station underground:\n text: south station underground\n south station amtrak:\n text: south station amtrak\n forest hills:\n text: forest hills\n riverside:\n text: riverside\n\nURI: TrainStopLocEnum
"},{"location":"TrainStopLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description end None mid None downtown None"},{"location":"TrainStopLocEnum/#slots","title":"Slots","text":"Name Description train_stop_loc The train stop collection location"},{"location":"TrainStopLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStopLocEnum/#schema-source","title":"Schema Source","text":"name: train_stop_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n end:\n text: end\n mid:\n text: mid\n downtown:\n text: downtown\n\nURI: xsd:string
base: str
uri: xsd:string
a complete URI
URI: xsd:anyURI
base: URI
uri: xsd:anyURI
repr: str
a URI or a CURIE
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
URI: VisMediaEnum
"},{"location":"VisMediaEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description photos None videos None commonly of the building None site context (adjacent buildings, vegetation, terrain, streets) None interiors None equipment None 3D scans None"},{"location":"VisMediaEnum/#slots","title":"Slots","text":"Name Description vis_media The building visual media"},{"location":"VisMediaEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"VisMediaEnum/#schema-source","title":"Schema Source","text":"name: vis_media_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n photos:\n text: photos\n videos:\n text: videos\n commonly of the building:\n text: commonly of the building\n site context (adjacent buildings, vegetation, terrain, streets):\n text: site context (adjacent buildings, vegetation, terrain, streets)\n interiors:\n text: interiors\n equipment:\n text: equipment\n 3D scans:\n text: 3D scans\n\nURI: WallConstTypeEnum
"},{"location":"WallConstTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description frame construction None joisted masonry None light noncombustible None masonry noncombustible None modified fire resistive None fire resistive None"},{"location":"WallConstTypeEnum/#slots","title":"Slots","text":"Name Description wall_const_type The building class of the wall defined by the composition of the building ele..."},{"location":"WallConstTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallConstTypeEnum/#schema-source","title":"Schema Source","text":"name: wall_const_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n frame construction:\n text: frame construction\n joisted masonry:\n text: joisted masonry\n light noncombustible:\n text: light noncombustible\n masonry noncombustible:\n text: masonry noncombustible\n modified fire resistive:\n text: modified fire resistive\n fire resistive:\n text: fire resistive\n\nURI: WallFinishMatEnum
"},{"location":"WallFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plaster None gypsum plaster None veneer plaster None gypsum board None tile None terrazzo None stone facing None acoustical treatment None wood None metal None masonry None"},{"location":"WallFinishMatEnum/#slots","title":"Slots","text":"Name Description wall_finish_mat The material utilized to finish the outer most layer of the wall"},{"location":"WallFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallFinishMatEnum/#schema-source","title":"Schema Source","text":"name: wall_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n plaster:\n text: plaster\n gypsum plaster:\n text: gypsum plaster\n veneer plaster:\n text: veneer plaster\n gypsum board:\n text: gypsum board\n tile:\n text: tile\n terrazzo:\n text: terrazzo\n stone facing:\n text: stone facing\n acoustical treatment:\n text: acoustical treatment\n wood:\n text: wood\n metal:\n text: metal\n masonry:\n text: masonry\n\nURI: WallLocEnum
"},{"location":"WallLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WallLocEnum/#slots","title":"Slots","text":"Name Description wall_loc The relative location of the wall within the room"},{"location":"WallLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallLocEnum/#schema-source","title":"Schema Source","text":"name: wall_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: WallSurfTreatmentEnum
"},{"location":"WallSurfTreatmentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description painted None wall paper None no treatment None paneling None stucco None fabric None"},{"location":"WallSurfTreatmentEnum/#slots","title":"Slots","text":"Name Description wall_surf_treatment The surface treatment of interior wall"},{"location":"WallSurfTreatmentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallSurfTreatmentEnum/#schema-source","title":"Schema Source","text":"name: wall_surf_treatment_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n painted:\n text: painted\n wall paper:\n text: wall paper\n no treatment:\n text: no treatment\n paneling:\n text: paneling\n stucco:\n text: stucco\n fabric:\n text: fabric\n\nURI: WallTextureEnum
"},{"location":"WallTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"WallTextureEnum/#slots","title":"Slots","text":"Name Description wall_texture The feel, appearance, or consistency of a wall surface"},{"location":"WallTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallTextureEnum/#schema-source","title":"Schema Source","text":"name: wall_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crows feet:\n text: crows feet\n crows-foot stomp:\n text: crows-foot stomp\n ? ''\n : text: ''\n double skip:\n text: double skip\n hawk and trowel:\n text: hawk and trowel\n knockdown:\n text: knockdown\n popcorn:\n text: popcorn\n orange peel:\n text: orange peel\n rosebud stomp:\n text: rosebud stomp\n Santa-Fe texture:\n text: Santa-Fe texture\n skip trowel:\n text: skip trowel\n smooth:\n text: smooth\n stomp knockdown:\n text: stomp knockdown\n swirl:\n text: swirl\n\nURI: WaterFeatTypeEnum
"},{"location":"WaterFeatTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fountain None pool None standing feature None stream None waterfall None"},{"location":"WaterFeatTypeEnum/#slots","title":"Slots","text":"Name Description water_feat_type The type of water feature present within the building being sampled"},{"location":"WaterFeatTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WaterFeatTypeEnum/#schema-source","title":"Schema Source","text":"name: water_feat_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n fountain:\n text: fountain\n pool:\n text: pool\n standing feature:\n text: standing feature\n stream:\n text: stream\n waterfall:\n text: waterfall\n\nURI: WeekdayEnum
"},{"location":"WeekdayEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Monday None Tuesday None Wednesday None Thursday None Friday None Saturday None Sunday None"},{"location":"WeekdayEnum/#slots","title":"Slots","text":"Name Description weekday The day of the week when sampling occurred"},{"location":"WeekdayEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WeekdayEnum/#schema-source","title":"Schema Source","text":"name: weekday_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Monday:\n text: Monday\n Tuesday:\n text: Tuesday\n Wednesday:\n text: Wednesday\n Thursday:\n text: Thursday\n Friday:\n text: Friday\n Saturday:\n text: Saturday\n Sunday:\n text: Sunday\n\nURI: WindowCondEnum
"},{"location":"WindowCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"WindowCondEnum/#slots","title":"Slots","text":"Name Description window_cond The physical condition of the window at the time of sampling"},{"location":"WindowCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCondEnum/#schema-source","title":"Schema Source","text":"name: window_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: WindowCoverEnum
"},{"location":"WindowCoverEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description blinds None curtains None none None"},{"location":"WindowCoverEnum/#slots","title":"Slots","text":"Name Description window_cover The type of window covering"},{"location":"WindowCoverEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCoverEnum/#schema-source","title":"Schema Source","text":"name: window_cover_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n blinds:\n text: blinds\n curtains:\n text: curtains\n none:\n text: none\n\nURI: WindowHorizPosEnum
"},{"location":"WindowHorizPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description left None middle None right None"},{"location":"WindowHorizPosEnum/#slots","title":"Slots","text":"Name Description window_horiz_pos The horizontal position of the window on the wall"},{"location":"WindowHorizPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowHorizPosEnum/#schema-source","title":"Schema Source","text":"name: window_horiz_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n left:\n text: left\n middle:\n text: middle\n right:\n text: right\n\nURI: WindowLocEnum
"},{"location":"WindowLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WindowLocEnum/#slots","title":"Slots","text":"Name Description window_loc The relative location of the window within the room"},{"location":"WindowLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowLocEnum/#schema-source","title":"Schema Source","text":"name: window_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: WindowMatEnum
"},{"location":"WindowMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clad None fiberglass None metal None vinyl None wood None"},{"location":"WindowMatEnum/#slots","title":"Slots","text":"Name Description window_mat The type of material used to finish a window"},{"location":"WindowMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowMatEnum/#schema-source","title":"Schema Source","text":"name: window_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n clad:\n text: clad\n fiberglass:\n text: fiberglass\n metal:\n text: metal\n vinyl:\n text: vinyl\n wood:\n text: wood\n\nURI: WindowTypeEnum
"},{"location":"WindowTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description single-hung sash window None horizontal sash window None fixed window None"},{"location":"WindowTypeEnum/#slots","title":"Slots","text":"Name Description window_type The type of windows"},{"location":"WindowTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowTypeEnum/#schema-source","title":"Schema Source","text":"name: window_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n single-hung sash window:\n text: single-hung sash window\n horizontal sash window:\n text: horizontal sash window\n fixed window:\n text: fixed window\n\nURI: WindowVertPosEnum
"},{"location":"WindowVertPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bottom None middle None top None low None high None"},{"location":"WindowVertPosEnum/#slots","title":"Slots","text":"Name Description window_vert_pos The vertical position of the window on the wall"},{"location":"WindowVertPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowVertPosEnum/#schema-source","title":"Schema Source","text":"name: window_vert_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bottom:\n text: bottom\n middle:\n text: middle\n top:\n text: top\n low:\n text: low\n high:\n text: high\n\nRepresents an instance of an execution of a particular workflow
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:WorkflowExecution
Note
Mermaid class diagram too large to render.
"},{"location":"WorkflowExecution/#inheritance","title":"Inheritance","text":"name: WorkflowExecution\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An analysis contains secondary analysis results derived from sequence\n reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) subclasses of WorkflowExecution is a distinct\n run with start and stop times, potentially with different inputs and outputs\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: PlannedProcess\nabstract: true\nslots:\n- ended_at_time\n- execution_resource\n- git_url\n- started_at_time\n- version\n- was_informed_by\nslot_usage:\n started_at_time:\n name: started_at_time\n required: true\n git_url:\n name: git_url\n required: true\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n execution_resource:\n name: execution_resource\n required: true\n was_informed_by:\n name: was_informed_by\n required: true\nclass_uri: nmdc:WorkflowExecution\nrules:\n- preconditions:\n slot_conditions:\n qc_status:\n name: qc_status\n equals_string: pass\n postconditions:\n slot_conditions:\n has_output:\n name: has_output\n required: true\n description: If qc_status has a value of pass, then the has_output slot is required.\n title: qc_status_pass_has_output_required\n- preconditions:\n slot_conditions:\n qc_status:\n name: qc_status\n value_presence: ABSENT\n postconditions:\n slot_conditions:\n has_output:\n name: has_output\n required: true\n description: If qc_status is not specified, then the has_output slot is required.\n title: qc_status_pass_null_has_output_required\n\nname: WorkflowExecution\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An analysis contains secondary analysis results derived from sequence\n reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) subclasses of WorkflowExecution is a distinct\n run with start and stop times, potentially with different inputs and outputs\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n started_at_time:\n name: started_at_time\n required: true\n git_url:\n name: git_url\n required: true\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n execution_resource:\n name: execution_resource\n required: true\n was_informed_by:\n name: was_informed_by\n required: true\nattributes:\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: WorkflowExecution\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: WorkflowExecution\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: WorkflowExecution\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: WorkflowExecution\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: WorkflowExecution\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:WorkflowExecution\nrules:\n- preconditions:\n slot_conditions:\n qc_status:\n name: qc_status\n equals_string: pass\n postconditions:\n slot_conditions:\n has_output:\n name: has_output\n required: true\n description: If qc_status has a value of pass, then the has_output slot is required.\n title: qc_status_pass_has_output_required\n- preconditions:\n slot_conditions:\n qc_status:\n name: qc_status\n value_presence: ABSENT\n postconditions:\n slot_conditions:\n has_output:\n name: has_output\n required: true\n description: If qc_status is not specified, then the has_output slot is required.\n title: qc_status_pass_null_has_output_required\n\nreplaces DnaDnaseEnum and DnaseRnaEnum
URI: YesNoEnum
"},{"location":"YesNoEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description no None yes None"},{"location":"YesNoEnum/#slots","title":"Slots","text":"Name Description dna_dnase dnase_rna"},{"location":"YesNoEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"YesNoEnum/#schema-source","title":"Schema Source","text":"name: YesNoEnum\ndescription: replaces DnaDnaseEnum and DnaseRnaEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 'no':\n text: 'no'\n 'yes':\n text: 'yes'\n\nThe work conducted by the National Microbiome Data Collaborative (https://ror.org/05cwx3318) is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).
"},{"location":"about/#framework","title":"Framework","text":"This schema was made using the LinkML framework. LinkML is a data modeling language that is used to create data models in a human-readable format. The LinkML framework is used to generate the schema in multiple formats, including JSON-LD, YAML, and RDF.
NMDC uses the LinkML framework to create a schema to be used by researchers, data scientists, and developers to understand the structure of the data and how it is related.
"},{"location":"about/#citing-nmdc","title":"Citing NMDC","text":""},{"location":"about/#schema","title":"Schema","text":"Microbiome Data Coordination Center. (n.d.). NMDC Schema. GitHub. from https://github.com/microbiomedata/nmdc-schema
"},{"location":"about/#program-launch","title":"Program Launch","text":"E. M. Wood-Charlson, Anubhav, D. Auberry, H. Blanco, M. I. Borkum, Y. E. Corilo, K. W. Davenport, S. Deshpande, R. Devarakonda, M. Drake, W. D. Duncan, M. C. Flynn, D. Hays, B. Hu, M. Huntemann, P.-E. Li, M. Lipton, C.-C. Lo, D. Millard, K. Miller, P. D. Piehowski, S. Purvine, T. B. K. Reddy, M. Shakya, J. C. Sundaramurthi, P. Vangay, Y. Wei, B. E. Wilson, S. Canon, P. S. G. Chain, K. Fagnan, S. Martin, L. A. McCue, C. J. Mungall, N. J. Mouncey, M. E. Maxon, E. A. Eloe-Fadrosh, The National Microbiome Data Collaborative: enabling microbiome science. Nature Reviews Microbiology 18, 313-314 (2020). doi: 10.1038/s41579-020-0377-0
"},{"location":"abs_air_humidity/","title":"Slot: absolute air humidity (abs_air_humidity)","text":"Actual mass of water vapor - mh20 - present in the air water vapor mixture
URI: MIXS:0000122
"},{"location":"abs_air_humidity/#inheritance","title":"Inheritance","text":"name: abs_air_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram, kilogram per kilogram, kilogram, pound\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Actual mass of water vapor - mh20 - present in the air water vapor mixture\ntitle: absolute air humidity\nexamples:\n- value: 9 gram per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- absolute air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000122\nalias: abs_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe date on which the information was added to the database.
URI: nmdc:add_date
"},{"location":"add_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Biosample Biological source material which can be characterized by an experiment no"},{"location":"add_date/#properties","title":"Properties","text":"name: add_date\ndescription: The date on which the information was added to the database.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: add_date\ndomain_of:\n- Biosample\n- DataGeneration\nrange: string\n\nAdditional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0001009
"},{"location":"add_recov_method/#inheritance","title":"Inheritance","text":"name: add_recov_method\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n for increase of hydrocarbon recovery from resource and start date for each one of\n them. If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: secondary and tertiary recovery methods and start date\nexamples:\n- value: Polymer Addition;2018-06-21T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary and tertiary recovery methods and start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001009\nalias: add_recov_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary
URI: MIXS:0000300
"},{"location":"additional_info/#inheritance","title":"Inheritance","text":"name: additional_info\nannotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information that doesn't fit anywhere else. Can also be used to propose\n new entries for fields with controlled vocabulary\ntitle: additional info\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- additional info\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000300\nalias: additional_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe street name and building number where the sampling occurred.
URI: MIXS:0000218
"},{"location":"address/#inheritance","title":"Inheritance","text":"name: address\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The street name and building number where the sampling occurred.\ntitle: address\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- address\nrank: 1000\nis_a: core field\nstring_serialization: '{integer}{text}'\nslot_uri: MIXS:0000218\nalias: address\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of rooms (room number, room name) immediately adjacent to the sampling room
URI: MIXS:0000219
"},{"location":"adj_room/#inheritance","title":"Inheritance","text":"name: adj_room\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of rooms (room number, room name) immediately adjacent to the sampling\n room\ntitle: adjacent rooms\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- adjacent rooms\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000219\nalias: adj_room\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nAerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together
URI: MIXS:0000773
"},{"location":"aero_struc/#inheritance","title":"Inheritance","text":"name: aero_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Aerospace structures typically consist of thin plates with stiffeners\n for the external surfaces, bulkheads and frames to support the shape and fasteners\n such as welds, rivets, screws and bolts to hold the components together\ntitle: aerospace structure\nexamples:\n- value: plane\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aerospace structure\nrank: 1000\nis_a: core field\nstring_serialization: '[plane|glider]'\nslot_uri: MIXS:0000773\nalias: aero_struc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nAddition of fertilizers, pesticides, etc. - amount and time of applications
URI: MIXS:0000639
"},{"location":"agrochem_addition/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: agrochem_addition\nannotations:\n expected_value:\n tag: expected_value\n value: agrochemical name;agrochemical amount;timestamp\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Addition of fertilizers, pesticides, etc. - amount and time of applications\ntitle: history/agrochemical additions\nexamples:\n- value: roundup;5 milligram per liter;2018-06-21\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/agrochemical additions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{timestamp}'\nslot_uri: MIXS:0000639\nalias: agrochem_addition\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM
URI: MIXS:0000108
"},{"location":"air_PM_concen/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: air_PM_concen\nannotations:\n expected_value:\n tag: expected_value\n value: particulate matter name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrograms per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances that remain suspended in the air, and comprise\n mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple\n PM's by entering numeric values preceded by name of PM\ntitle: air particulate matter concentration\nexamples:\n- value: PM2.5;10 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air particulate matter concentration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000108\nalias: air_PM_concen\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTemperature of the air at the time of sampling
URI: MIXS:0000124
"},{"location":"air_temp/#inheritance","title":"Inheritance","text":"name: air_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature of the air at the time of sampling\ntitle: air temperature\nexamples:\n- value: 20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000124\nalias: air_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens
URI: MIXS:0000551
"},{"location":"air_temp_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: air_temp_regm\nannotations:\n expected_value:\n tag: expected_value\n value: temperature value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to varying temperatures;\n should include the temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include different temperature regimens\ntitle: air temperature regimen\nexamples:\n- value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000551\nalias: air_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAluminum saturation (esp. For tropical soils)
URI: MIXS:0000607
"},{"location":"al_sat/#inheritance","title":"Inheritance","text":"name: al_sat\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Aluminum saturation (esp. For tropical soils)\ntitle: extreme_unusual_properties/Al saturation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000607\nalias: al_sat\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining Al saturation
URI: MIXS:0000324
"},{"location":"al_sat_meth/#inheritance","title":"Inheritance","text":"name: al_sat_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or URL\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining Al saturation\ntitle: extreme_unusual_properties/Al saturation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000324\nalias: al_sat_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nAlkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
URI: MIXS:0000421
"},{"location":"alkalinity/#inheritance","title":"Inheritance","text":"name: alkalinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliequivalent per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Alkalinity, the ability of a solution to neutralize acids to the equivalence\n point of carbonate or bicarbonate\ntitle: alkalinity\nexamples:\n- value: 50 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000421\nalias: alkalinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMethod used for alkalinity measurement
URI: MIXS:0000298
"},{"location":"alkalinity_method/#inheritance","title":"Inheritance","text":"name: alkalinity_method\nannotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method used for alkalinity measurement\ntitle: alkalinity method\nexamples:\n- value: titration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000298\nalias: alkalinity_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of alkyl diethers
URI: MIXS:0000490
"},{"location":"alkyl_diethers/#inheritance","title":"Inheritance","text":"name: alkyl_diethers\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of alkyl diethers\ntitle: alkyl diethers\nexamples:\n- value: 0.005 mole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkyl diethers\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000490\nalias: alkyl_diethers\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nthe list of protein identifiers that are associated with the peptide sequence
URI: nmdc:all_proteins
","text":""},{"location":"all_proteins/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"all_proteins/#properties","title":"Properties","text":"Range: GeneProduct
Multivalued: True
name: all_proteins\ndescription: the list of protein identifiers that are associated with the peptide\n sequence\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: all_proteins\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\nmultivalued: true\n\nAltitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air
URI: MIXS:0000094
"},{"location":"alt/#inheritance","title":"Inheritance","text":"name: alt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: Altitude is a term used to identify heights of objects such as airplanes,\n space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric\n layers and clouds. It is used to measure the height of an object which is above\n the earth's surface. In this context, the altitude measurement is the vertical distance\n between the earth's surface above sea level and the sampled position in the air\ntitle: altitude\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- altitude\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000094\nalias: alt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nA list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.
URI: nmdc:alternative_descriptions
"},{"location":"alternative_descriptions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_descriptions/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_descriptions\ndescription: A list of alternative descriptions for the entity. The distinction between\n description and alternative descriptions is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternative_descriptions\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\nA list of alternative identifiers for the entity.
URI: nmdc:alternative_identifiers
"},{"location":"alternative_identifiers/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$
name: alternative_identifiers\ndescription: A list of alternative identifiers for the entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternative_identifiers\ndomain_of:\n- MetaboliteIdentification\n- NamedThing\nrange: uriorcurie\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n\nA list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.
URI: nmdc:alternative_names
"},{"location":"alternative_names/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EnvironmentalMaterialTerm no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no OntologyClass A representation of class defined in an external ontology no OrthologyGroup A set of genes or gene products in which all members are orthologous no Study A study summarizes the overall goal of a research initiative and outlines the... yes Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"alternative_names/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_names\ndescription: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\n- skos:altLabel\nrank: 1000\nalias: alternative_names\ndomain_of:\n- OntologyClass\n- Study\nrange: string\nmultivalued: true\n\nA list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.
URI: nmdc:alternative_titles
"},{"location":"alternative_titles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_titles/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_titles\ndescription: A list of alternative titles for the entity. The distinction between\n title and alternative titles is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\nrank: 1000\nalias: alternative_titles\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\nMeasurement of aminopeptidase activity
URI: MIXS:0000172
"},{"location":"aminopept_act/#inheritance","title":"Inheritance","text":"name: aminopept_act\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of aminopeptidase activity\ntitle: aminopeptidase activity\nexamples:\n- value: 0.269 mole per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aminopeptidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000172\nalias: aminopept_act\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of ammonium in the sample
URI: MIXS:0000427
"},{"location":"ammonium/#inheritance","title":"Inheritance","text":"name: ammonium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ammonium in the sample\ntitle: ammonium\nexamples:\n- value: 1.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ammonium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000427\nalias: ammonium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of ammonium nitrogen in the sample
URI: nmdc:ammonium_nitrogen
"},{"location":"ammonium_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ammonium_nitrogen/#properties","title":"Properties","text":"name: ammonium_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ammonium nitrogen in the sample\ntitle: ammonium nitrogen\nexamples:\n- value: 2.3 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- ammonium_nitrogen\n- NH4-N\nrank: 1000\nalias: ammonium_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe unit of illuminance and luminous emittance, measuring luminous flux per unit area
URI: MIXS:0000140
"},{"location":"amount_light/#inheritance","title":"Inheritance","text":"name: amount_light\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux, lumens per square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The unit of illuminance and luminous emittance, measuring luminous flux\n per unit area\ntitle: amount of light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount of light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000140\nalias: amount_light\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:analysis_identifiers
"},{"location":"analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: analysis_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nSelect all the data types associated or available for this biosample
URI: nmdc:analysis_type
"},{"location":"analysis_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"analysis_type/#properties","title":"Properties","text":"Range: AnalysisTypeEnum
Multivalued: True
Recommended: True
name: analysis_type\ndescription: Select all the data types associated or available for this biosample\ntitle: analysis/data type\nexamples:\n- value: metagenomics; metabolomics; metaproteomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIxS:investigation_type\nrank: 3\nalias: analysis_type\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: AnalysisTypeEnum\nrecommended: true\nmultivalued: true\n\nThe type of analyte(s) that were measured in the data generation process and analyzed
_ in the Workflow Chain_
__
URI: nmdc:analyte_category
"},{"location":"analyte_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated yes"},{"location":"analyte_category/#properties","title":"Properties","text":"Range: String
Required: True
name: analyte_category\ndescription: \"The type of analyte(s) that were measured in the data generation process\\\n \\ and analyzed\\n in the Workflow Chain\\n\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: analyte_category\ndomain_of:\n- DataGeneration\nrange: string\nrequired: true\n\nInformation about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)
URI: MIXS:0000247
"},{"location":"ances_data/#inheritance","title":"Inheritance","text":"name: ances_data\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about either pedigree or other ancestral information description\n (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A\n x B) x B] x B)\ntitle: ancestral data\nexamples:\n- value: A/3*B\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ancestral data\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000247\nalias: ances_data\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.
URI: MIXS:0000644
"},{"location":"annual_precpt/#inheritance","title":"Inheritance","text":"name: annual_precpt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of all annual precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean annual precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000644\nalias: annual_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMean annual temperature
URI: MIXS:0000642
"},{"location":"annual_temp/#inheritance","title":"Inheritance","text":"name: annual_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Mean annual temperature\ntitle: mean annual temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000642\nalias: annual_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens
URI: MIXS:0000553
"},{"location":"antibiotic_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: antibiotic_regm\nannotations:\n expected_value:\n tag: expected_value\n value: antibiotic name;antibiotic amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving antibiotic administration; should\n include the name of antibiotic, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple antibiotic regimens\ntitle: antibiotic regimen\nexamples:\n- value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- antibiotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000553\nalias: antibiotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAPI gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)
URI: MIXS:0000157
"},{"location":"api/#inheritance","title":"Inheritance","text":"name: api\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degrees API\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'API gravity is a measure of how heavy or light a petroleum liquid is\n compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e\n API)'\ntitle: API gravity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- API gravity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000157\nalias: api\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:applied_roles
"},{"location":"applied_roles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applied_roles/#properties","title":"Properties","text":"Range: CreditEnum
Multivalued: True
Required: True
name: applied_roles\nannotations:\n tooltip:\n tag: tooltip\n value: 'Identify all CRediT roles associated with this contributor. CRediT Information:\n https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: applied_roles\ndomain_of:\n- CreditAssociation\nrange: CreditEnum\nrequired: true\nmultivalued: true\n\nURI: nmdc:applies_to_person
"},{"location":"applies_to_person/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applies_to_person/#properties","title":"Properties","text":"Range: PersonValue
Required: True
name: applies_to_person\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: applies_to_person\ndomain_of:\n- CreditAssociation\nrange: PersonValue\nrequired: true\n\nAn architectural structure is a human-made, free-standing, immobile outdoor construction
URI: MIXS:0000774
"},{"location":"arch_struc/#inheritance","title":"Inheritance","text":"name: arch_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: An architectural structure is a human-made, free-standing, immobile outdoor\n construction\ntitle: architectural structure\nexamples:\n- value: shed\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- architectural structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000774\nalias: arch_struc\ndomain_of:\n- Biosample\nrange: arch_struc_enum\nmultivalued: false\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000133
"},{"location":"aromatics_pc/#inheritance","title":"Inheritance","text":"name: aromatics_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: aromatics wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aromatics wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000133\nalias: aromatics_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA score for comparing metagenomic assembly quality from same sample.
URI: nmdc:asm_score
"},{"location":"asm_score/#inheritance","title":"Inheritance","text":"name: asm_score\ndescription: A score for comparing metagenomic assembly quality from same sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: asm_score\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000135
"},{"location":"asphaltenes_pc/#inheritance","title":"Inheritance","text":"name: asphaltenes_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: asphaltenes wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- asphaltenes wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000135\nalias: asphaltenes_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:assembly_identifiers
"},{"location":"assembly_identifiers/#inheritance","title":"Inheritance","text":"name: assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: assembly_identifiers\nrange: string\n\nA list of DOIs associated with a resource, such as a list of DOIS associated with a Study.
URI: nmdc:associated_dois
"},{"location":"associated_dois/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"associated_dois/#properties","title":"Properties","text":"Range: Doi
Multivalued: True
name: associated_dois\ndescription: A list of DOIs associated with a resource, such as a list of DOIS associated\n with a Study.\nexamples:\n- value: '[{''doi'': ''doi:10.46936/intm.proj.2021.60141/60000423'', ''doi_provider'':\n ''emsl'', ''doi_category'': ''award_doi''}, {''doi'': ''doi:10.1101/2022.12.12.520098'',\n ''doi_category'': ''publication_doi''}, {''doi'': ''doi:10.48321/D1Z60Q'', ''doi_category'':\n ''data_management_plan_doi'', ''doi_provider'': ''gsc''}]'\n description: Provides a list of two DOIs; specifically, an EMSL award DOI and a\n publication DOI.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Associated DOIs\n- Associated digital object identifiers\nrank: 1000\nalias: associated_dois\ndomain_of:\n- Study\nrange: Doi\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe study associated with a resource.
URI: nmdc:associated_studies
"},{"location":"associated_studies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Biosample Biological source material which can be characterized by an experiment yes"},{"location":"associated_studies/#properties","title":"Properties","text":"Range: Study
Multivalued: True
Required: True
name: associated_studies\ndescription: The study associated with a resource.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: associated_studies\ndomain_of:\n- Biosample\n- DataGeneration\nrange: Study\nrequired: true\nmultivalued: true\nstructured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n\nMeasurement of atmospheric data; can include multiple data
URI: MIXS:0001097
"},{"location":"atmospheric_data/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: atmospheric_data\nannotations:\n expected_value:\n tag: expected_value\n value: atmospheric data name;measurement value\n occurrence:\n tag: occurrence\n value: m\ndescription: Measurement of atmospheric data; can include multiple data\ntitle: atmospheric data\nexamples:\n- value: wind speed;9 knots\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- atmospheric data\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0001097\nalias: atmospheric_data\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day
URI: MIXS:0000141
"},{"location":"avg_dew_point/#inheritance","title":"Inheritance","text":"name: avg_dew_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of dew point measures taken at the beginning of every hour\n over a 24 hour period on the sampling day\ntitle: average dew point\nexamples:\n- value: 25.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000141\nalias: avg_dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDaily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.
URI: MIXS:0000775
"},{"location":"avg_occup/#inheritance","title":"Inheritance","text":"name: avg_occup\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Daily average occupancy of room. Indicate the number of person(s) daily\n occupying the sampling room.\ntitle: average daily occupancy\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average daily occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000775\nalias: avg_occup\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day
URI: MIXS:0000142
"},{"location":"avg_temp/#inheritance","title":"Inheritance","text":"name: avg_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of temperatures taken at the beginning of every hour over\n a 24 hour period on the sampling day\ntitle: average temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000142\nalias: avg_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nBacterial production in the water column measured by isotope uptake
URI: MIXS:0000683
"},{"location":"bac_prod/#inheritance","title":"Inheritance","text":"name: bac_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Bacterial production in the water column measured by isotope uptake\ntitle: bacterial production\nexamples:\n- value: 5 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000683\nalias: bac_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of bacterial respiration in the water column
URI: MIXS:0000684
"},{"location":"bac_resp/#inheritance","title":"Inheritance","text":"name: bac_resp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, micromole oxygen per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of bacterial respiration in the water column\ntitle: bacterial respiration\nexamples:\n- value: 300 micromole oxygen per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial respiration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000684\nalias: bac_resp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of bacterial carbon production
URI: MIXS:0000173
"},{"location":"bacteria_carb_prod/#inheritance","title":"Inheritance","text":"name: bacteria_carb_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of bacterial carbon production\ntitle: bacterial carbon production\nexamples:\n- value: 2.53 microgram per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial carbon production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000173\nalias: bacteria_carb_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nForce per unit area exerted against a surface by the weight of air above that surface
URI: MIXS:0000096
"},{"location":"barometric_press/#inheritance","title":"Inheritance","text":"name: barometric_press\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millibar\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Force per unit area exerted against a surface by the weight of air above\n that surface\ntitle: barometric pressure\nexamples:\n- value: 5 millibar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- barometric pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000096\nalias: barometric_press\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nName of the basin (e.g. Campos)
URI: MIXS:0000290
"},{"location":"basin/#inheritance","title":"Inheritance","text":"name: basin\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the basin (e.g. Campos)\ntitle: basin name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- basin name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000290\nalias: basin\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe number of bathrooms in the building
URI: MIXS:0000776
"},{"location":"bathroom_count/#inheritance","title":"Inheritance","text":"name: bathroom_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of bathrooms in the building\ntitle: bathroom count\nexamples:\n- value: '1'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bathroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000776\nalias: bathroom_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe number of bedrooms in the building
URI: MIXS:0000777
"},{"location":"bedroom_count/#inheritance","title":"Inheritance","text":"name: bedroom_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of bedrooms in the building\ntitle: bedroom count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bedroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000777\nalias: bedroom_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of benzene in the sample
URI: MIXS:0000153
"},{"location":"benzene/#inheritance","title":"Inheritance","text":"name: benzene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of benzene in the sample\ntitle: benzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- benzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000153\nalias: benzene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nthe specific protein identifier most correctly associated with the peptide sequence
URI: nmdc:best_protein
","text":""},{"location":"best_protein/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"best_protein/#properties","title":"Properties","text":"name: best_protein\ndescription: the specific protein identifier most correctly associated with the peptide\n sequence\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: best_protein\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\n\nName of the metagenome-assembled genome.
URI: nmdc:bin_name
"},{"location":"bin_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_name/#properties","title":"Properties","text":"Range: String
Required: True
name: bin_name\ndescription: Name of the metagenome-assembled genome.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_name\ndomain_of:\n- MagBin\nrange: string\nrequired: true\n\nThe quality of the metagenome-assembled genome based on MIMAG standards (https://doi.org/10.1038/nbt.3893).
URI: nmdc:bin_quality
"},{"location":"bin_quality/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_quality/#properties","title":"Properties","text":"name: bin_quality\ndescription: The quality of the metagenome-assembled genome based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_quality\ndomain_of:\n- MagBin\nrange: BinQualityEnum\n\nNumber of contigs that ended up in a medium or high quality bin.
URI: nmdc:binned_contig_num
"},{"location":"binned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"binned_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: binned_contig_num\ndescription: Number of contigs that ended up in a medium or high quality bin.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: binned_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nAmount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period
URI: MIXS:0000653
"},{"location":"biochem_oxygen_dem/#inheritance","title":"Inheritance","text":"name: biochem_oxygen_dem\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Amount of dissolved oxygen needed by aerobic biological organisms in\n a body of water to break down organic material present in a given water sample at\n certain temperature over a specific time period\ntitle: biochemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biochemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000653\nalias: biochem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nList of biocides (commercial name of product and supplier) and date of administration
URI: MIXS:0001011
"},{"location":"biocide/#inheritance","title":"Inheritance","text":"name: biocide\nannotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of biocides (commercial name of product and supplier) and date of\n administration\ntitle: biocide administration\nexamples:\n- value: ALPHA 1427;Baker Hughes;2008-01-23\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001011\nalias: biocide\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMethod of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)
URI: MIXS:0000456
"},{"location":"biocide_admin_method/#inheritance","title":"Inheritance","text":"name: biocide_admin_method\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method of biocide administration (dose, frequency, duration, time elapsed\n between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)\ntitle: biocide administration method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\nslot_uri: MIXS:0000456\nalias: biocide_admin_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:biogas_retention_time
"},{"location":"biogas_retention_time/#properties","title":"Properties","text":"name: biogas_retention_time\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_retention_time\nrange: string\n\nURI: nmdc:biogas_temperature
"},{"location":"biogas_temperature/#properties","title":"Properties","text":"name: biogas_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_temperature\nrange: string\n\nThe level of genome modification.
URI: MIXS:0000858
"},{"location":"biol_stat/#inheritance","title":"Inheritance","text":"name: biol_stat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The level of genome modification.\ntitle: biological status\nexamples:\n- value: natural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000858\nalias: biol_stat\ndomain_of:\n- Biosample\nrange: biol_stat_enum\nmultivalued: false\n\nAmount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements
URI: MIXS:0000174
"},{"location":"biomass/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: biomass\nannotations:\n expected_value:\n tag: expected_value\n value: biomass type;measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n e.g. Microbial, total. Can include multiple measurements\ntitle: biomass\nexamples:\n- value: total;20 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biomass\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000174\nalias: biomass\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:biomaterial_purity
"},{"location":"biomaterial_purity/#inheritance","title":"Inheritance","text":"name: biomaterial_purity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biomaterial_purity\ndomain_of:\n- ProcessedSample\nrange: QuantityValue\n\nURI: nmdc:biosample_categories
"},{"location":"biosample_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biosample_categories/#properties","title":"Properties","text":"Range: BiosampleCategoryEnum
Multivalued: True
name: biosample_categories\ntitle: Categories the biosample belongs to\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biosample_categories\ndomain_of:\n- Biosample\nrange: BiosampleCategoryEnum\nmultivalued: true\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:biosample_identifiers
"},{"location":"biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: biosample_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThis property links a database object to the set of samples within it.
URI: nmdc:biosample_set
"},{"location":"biosample_set/#inheritance","title":"Inheritance","text":"Range: Biosample
Multivalued: True
name: biosample_set\ndescription: This property links a database object to the set of samples within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: biosample_set\ndomain_of:\n- Database\nrange: Biosample\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nInformation about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.
URI: MIXS:0001038
"},{"location":"biotic_regm/#inheritance","title":"Inheritance","text":"name: biotic_regm\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about treatment(s) involving use of biotic factors, such\n as bacteria, viruses or fungi.\ntitle: biotic regimen\nexamples:\n- value: sample inoculated with Rhizobium spp. Culture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001038\nalias: biotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDescription of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object
URI: MIXS:0000028
"},{"location":"biotic_relationship/#inheritance","title":"Inheritance","text":"name: biotic_relationship\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\ndescription: Description of relationship(s) between the subject organism and other\n organism(s) it is associated with. E.g., parasite on species X; mutualist with species\n Y. The target organism is the subject of the relationship, and the other organism(s)\n is the object\ntitle: observed biotic relationship\nexamples:\n- value: free living\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed biotic relationship\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000028\nalias: biotic_relationship\ndomain_of:\n- Biosample\nrange: biotic_relationship_enum\nmultivalued: false\n\nConcentration of bishomohopanol
URI: MIXS:0000175
"},{"location":"bishomohopanol/#inheritance","title":"Inheritance","text":"name: bishomohopanol\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, microgram per gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of bishomohopanol\ntitle: bishomohopanol\nexamples:\n- value: 14 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bishomohopanol\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000175\nalias: bishomohopanol\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nResting diastolic blood pressure, measured as mm mercury
URI: MIXS:0000258
"},{"location":"blood_press_diast/#inheritance","title":"Inheritance","text":"name: blood_press_diast\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Resting diastolic blood pressure, measured as mm mercury\ntitle: host blood pressure diastolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure diastolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000258\nalias: blood_press_diast\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nResting systolic blood pressure, measured as mm mercury
URI: MIXS:0000259
"},{"location":"blood_press_syst/#inheritance","title":"Inheritance","text":"name: blood_press_syst\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Resting systolic blood pressure, measured as mm mercury\ntitle: host blood pressure systolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure systolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000259\nalias: blood_press_syst\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of bromide
URI: MIXS:0000176
"},{"location":"bromide/#inheritance","title":"Inheritance","text":"name: bromide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of bromide\ntitle: bromide\nexamples:\n- value: 0.05 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bromide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000176\nalias: bromide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe building design, construction and operation documents
URI: MIXS:0000787
"},{"location":"build_docs/#inheritance","title":"Inheritance","text":"name: build_docs\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building design, construction and operation documents\ntitle: design, construction, and operation documents\nexamples:\n- value: maintenance plans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- design, construction, and operation documents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000787\nalias: build_docs\ndomain_of:\n- Biosample\nrange: build_docs_enum\nmultivalued: false\n\nThe primary function for which a building or discrete part of a building is intended to be used
URI: MIXS:0000761
"},{"location":"build_occup_type/#inheritance","title":"Inheritance","text":"Range: BuildOccupTypeEnum
Multivalued: True
name: build_occup_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: The primary function for which a building or discrete part of a building\n is intended to be used\ntitle: building occupancy type\nexamples:\n- value: market\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building occupancy type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000761\nalias: build_occup_type\ndomain_of:\n- Biosample\nrange: build_occup_type_enum\nmultivalued: true\n\nA location (geography) where a building is set
URI: MIXS:0000768
"},{"location":"building_setting/#inheritance","title":"Inheritance","text":"name: building_setting\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A location (geography) where a building is set\ntitle: building setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building setting\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000768\nalias: building_setting\ndomain_of:\n- Biosample\nrange: building_setting_enum\nmultivalued: false\n\nThe age of the built structure since construction
URI: MIXS:0000145
"},{"location":"built_struc_age/#inheritance","title":"Inheritance","text":"name: built_struc_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The age of the built structure since construction\ntitle: built structure age\nexamples:\n- value: '15'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000145\nalias: built_struc_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe characterization of the location of the built structure as high or low human density
URI: MIXS:0000778
"},{"location":"built_struc_set/#inheritance","title":"Inheritance","text":"name: built_struc_set\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The characterization of the location of the built structure as high or\n low human density\ntitle: built structure setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure setting\nrank: 1000\nis_a: core field\nstring_serialization: '[urban|rural]'\nslot_uri: MIXS:0000778\nalias: built_struc_set\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads
URI: MIXS:0000721
"},{"location":"built_struc_type/#inheritance","title":"Inheritance","text":"name: built_struc_type\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A physical structure that is a body or assemblage of bodies in space\n to form a system capable of supporting loads\ntitle: built structure type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000721\nalias: built_struc_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nElectrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.
URI: nmdc:bulk_elect_conductivity
"},{"location":"bulk_elect_conductivity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bulk_elect_conductivity/#properties","title":"Properties","text":"name: bulk_elect_conductivity\ndescription: Electrical conductivity is a measure of the ability to carry electric\n current, which is mostly dictated by the chemistry of and amount of water.\ntitle: bulk electrical conductivity\ncomments:\n- Provide the value output of the field instrument.\nexamples:\n- value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')\n description: The conductivity measurement was 0.017 millisiemens per centimeter.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bulk_elect_conductivity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of calcium in the sample
URI: MIXS:0000432
"},{"location":"calcium/#inheritance","title":"Inheritance","text":"name: calcium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of calcium in the sample\ntitle: calcium\nexamples:\n- value: 0.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- calcium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000432\nalias: calcium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nthe file containing calibration data object
URI: nmdc:calibration_object
"},{"location":"calibration_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process no"},{"location":"calibration_object/#properties","title":"Properties","text":"name: calibration_object\ndescription: the file containing calibration data object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_object\ndomain_of:\n- CalibrationInformation\nrange: DataObject\nstructured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n\nThis property links a database object to the set of calibrations within it.
URI: nmdc:calibration_set
"},{"location":"calibration_set/#inheritance","title":"Inheritance","text":"Range: CalibrationInformation
Multivalued: True
name: calibration_set\ndescription: This property links a database object to the set of calibrations within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: calibration_set\ndomain_of:\n- Database\nrange: CalibrationInformation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nthe reference standard(s) used for calibration
URI: nmdc:calibration_standard
"},{"location":"calibration_standard/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process no"},{"location":"calibration_standard/#properties","title":"Properties","text":"name: calibration_standard\ndescription: the reference standard(s) used for calibration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_standard\ndomain_of:\n- CalibrationInformation\nrange: CalibrationStandardEnum\n\nthe target measurement of the calibration
URI: nmdc:calibration_target
"},{"location":"calibration_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process yes"},{"location":"calibration_target/#properties","title":"Properties","text":"name: calibration_target\ndescription: the target measurement of the calibration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_target\ndomain_of:\n- CalibrationInformation\nrange: CalibrationTargetEnum\n\nCarbon dioxide (gas) amount or concentration at the time of sampling
URI: MIXS:0000097
"},{"location":"carb_dioxide/#inheritance","title":"Inheritance","text":"name: carb_dioxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Carbon dioxide (gas) amount or concentration at the time of sampling\ntitle: carbon dioxide\nexamples:\n- value: 410 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000097\nalias: carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCarbon monoxide (gas) amount or concentration at the time of sampling
URI: MIXS:0000098
"},{"location":"carb_monoxide/#inheritance","title":"Inheritance","text":"name: carb_monoxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Carbon monoxide (gas) amount or concentration at the time of sampling\ntitle: carbon monoxide\nexamples:\n- value: 0.1 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon monoxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000098\nalias: carb_monoxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nRatio of amount or concentrations of carbon to nitrogen
URI: MIXS:0000310
"},{"location":"carb_nitro_ratio/#inheritance","title":"Inheritance","text":"name: carb_nitro_ratio\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ratio of amount or concentrations of carbon to nitrogen\ntitle: carbon/nitrogen ratio\nexamples:\n- value: '0.417361111'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon/nitrogen ratio\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000310\nalias: carb_nitro_ratio\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe area of the ceiling space within the room
URI: MIXS:0000148
"},{"location":"ceil_area/#inheritance","title":"Inheritance","text":"name: ceil_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The area of the ceiling space within the room\ntitle: ceiling area\nexamples:\n- value: 25 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000148\nalias: ceil_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000779
"},{"location":"ceil_cond/#inheritance","title":"Inheritance","text":"name: ceil_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the ceiling at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\ntitle: ceiling condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000779\nalias: ceil_cond\ndomain_of:\n- Biosample\nrange: ceil_cond_enum\nmultivalued: false\n\nThe type of material used to finish a ceiling
URI: MIXS:0000780
"},{"location":"ceil_finish_mat/#inheritance","title":"Inheritance","text":"name: ceil_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material used to finish a ceiling\ntitle: ceiling finish material\nexamples:\n- value: stucco\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000780\nalias: ceil_finish_mat\ndomain_of:\n- Biosample\nrange: ceil_finish_mat_enum\nmultivalued: false\n\nThe construction format of the ceiling
URI: MIXS:0000782
"},{"location":"ceil_struc/#inheritance","title":"Inheritance","text":"name: ceil_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The construction format of the ceiling\ntitle: ceiling structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling structure\nrank: 1000\nis_a: core field\nstring_serialization: '[wood frame|concrete]'\nslot_uri: MIXS:0000782\nalias: ceil_struc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe feel, appearance, or consistency of a ceiling surface
URI: MIXS:0000783
"},{"location":"ceil_texture/#inheritance","title":"Inheritance","text":"name: ceil_texture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The feel, appearance, or consistency of a ceiling surface\ntitle: ceiling texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000783\nalias: ceil_texture\ndomain_of:\n- Biosample\nrange: ceil_texture_enum\nmultivalued: false\n\nThe ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow
URI: MIXS:0000143
"},{"location":"ceil_thermal_mass/#inheritance","title":"Inheritance","text":"name: ceil_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the ceiling to provide inertia against temperature fluctuations.\n Generally this means concrete that is exposed. A metal deck that supports a concrete\n slab will act thermally as long as it is exposed to room air flow\ntitle: ceiling thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000143\nalias: ceil_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of ceiling according to the ceiling's appearance or construction
URI: MIXS:0000784
"},{"location":"ceil_type/#inheritance","title":"Inheritance","text":"name: ceil_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of ceiling according to the ceiling's appearance or construction\ntitle: ceiling type\nexamples:\n- value: coffered\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000784\nalias: ceil_type\ndomain_of:\n- Biosample\nrange: ceil_type_enum\nmultivalued: false\n\nSigns of the presence of mold or mildew on the ceiling
URI: MIXS:0000781
"},{"location":"ceil_water_mold/#inheritance","title":"Inheritance","text":"name: ceil_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the ceiling\ntitle: ceiling signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000781\nalias: ceil_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
URI: MIXS:0000751
"},{"location":"chem_administration/#inheritance","title":"Inheritance","text":"Range: ControlledTermValue
Multivalued: True
name: chem_administration\nannotations:\n expected_value:\n tag: expected_value\n value: CHEBI;timestamp\n occurrence:\n tag: occurrence\n value: m\ndescription: List of chemical compounds administered to the host or site where sampling\n occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple\n compounds. For chemical entities of biological interest ontology (chebi) (v 163),\n http://purl.bioontology.org/ontology/chebi\ntitle: chemical administration\nexamples:\n- value: agar [CHEBI:2509];2018-05-11T20:00Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical administration\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]};{timestamp}'\nslot_uri: MIXS:0000751\nalias: chem_administration\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTreatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens
URI: MIXS:0000555
"},{"location":"chem_mutagen/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: chem_mutagen\nannotations:\n expected_value:\n tag: expected_value\n value: mutagen name;mutagen amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving use of mutagens; should include the name of mutagen,\n amount administered, treatment regimen including how many times the treatment was\n repeated, how long each treatment lasted, and the start and end time of the entire\n treatment; can include multiple mutagen regimens\ntitle: chemical mutagen\nexamples:\n- value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical mutagen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000555\nalias: chem_mutagen\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite
URI: MIXS:0000656
"},{"location":"chem_oxygen_dem/#inheritance","title":"Inheritance","text":"name: chem_oxygen_dem\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A measure of the capacity of water to consume oxygen during the decomposition\n of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite\ntitle: chemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000656\nalias: chem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMethod of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)
URI: MIXS:0000457
"},{"location":"chem_treat_method/#inheritance","title":"Inheritance","text":"name: chem_treat_method\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method of chemical administration(dose, frequency, duration, time elapsed\n between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)\ntitle: chemical treatment method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\nslot_uri: MIXS:0000457\nalias: chem_treat_method\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nList of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included
URI: MIXS:0001012
"},{"location":"chem_treatment/#inheritance","title":"Inheritance","text":"name: chem_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of chemical compounds administered upstream the sampling location\n where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n demulsifiers, and other production chemicals etc.). The commercial name of the product\n and name of the supplier should be provided. The date of administration should also\n be included\ntitle: chemical treatment\nexamples:\n- value: ACCENT 1125;DOW;2010-11-17\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001012\nalias: chem_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe type of chemical conversion process.
URI: nmdc:chemical_conversion_category
"},{"location":"chemical_conversion_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no"},{"location":"chemical_conversion_category/#properties","title":"Properties","text":"name: chemical_conversion_category\ndescription: The type of chemical conversion process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_conversion_category\ndomain_of:\n- ChemicalConversionProcess\nrange: ChemicalConversionCategoryEnum\n\nThis property links a database object to the set of chemical entities within it.
URI: nmdc:chemical_entity_set
","text":""},{"location":"chemical_entity_set/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: chemical_entity_set\ndescription: This property links a database object to the set of chemical entities\n within it.\ndeprecated: Deprecation of the ChemicalEntity class, means deprecation of the chemical_entity_set\n as well.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: chemical_entity_set\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA generic grouping for molecular formulae and empirical formulae
URI: nmdc:chemical_formula
"},{"location":"chemical_formula/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"chemical_formula/#properties","title":"Properties","text":"name: chemical_formula\ndescription: A generic grouping for molecular formulae and empirical formulae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_formula\ndomain_of:\n- ChemicalEntity\nrange: string\n\nTool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.
URI: MIXS:0000052
"},{"location":"chimera_check/#inheritance","title":"Inheritance","text":"name: chimera_check\nannotations:\n expected_value:\n tag: expected_value\n value: name and version of software, parameters used\ndescription: Tool(s) used for chimera checking, including version number and parameters,\n to discover and remove chimeric sequences. A chimeric sequence is comprised of two\n or more phylogenetically distinct parent sequences.\ntitle: chimera check software\nexamples:\n- value: uchime;v4.1;default parameters\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chimera check software\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{software};{version};{parameters}'\nslot_uri: MIXS:0000052\nalias: chimera_check\nrange: TextValue\nmultivalued: false\n\nConcentration of chloride in the sample
URI: MIXS:0000429
"},{"location":"chloride/#inheritance","title":"Inheritance","text":"name: chloride\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of chloride in the sample\ntitle: chloride\nexamples:\n- value: 5000 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chloride\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000429\nalias: chloride\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of chlorophyll
URI: MIXS:0000177
"},{"location":"chlorophyll/#inheritance","title":"Inheritance","text":"name: chlorophyll\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter, microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of chlorophyll\ntitle: chlorophyll\nexamples:\n- value: 5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chlorophyll\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000177\nalias: chlorophyll\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of chromatography used in a process.
URI: nmdc:chromatographic_category
"},{"location":"chromatographic_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no"},{"location":"chromatographic_category/#properties","title":"Properties","text":"name: chromatographic_category\ndescription: The type of chromatography used in a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chromatographic_category\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: ChromatographicCategoryEnum\n\nTreatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates
URI: MIXS:0001040
"},{"location":"climate_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: climate_environment\nannotations:\n expected_value:\n tag: expected_value\n value: climate name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to a particular climate; treatment regimen\n including how many times the treatment was repeated, how long each treatment lasted,\n and the start and end time of the entire treatment; can include multiple climates\ntitle: climate environment\nexamples:\n- value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- climate environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001040\nalias: climate_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nNMDC Schema is a collaborative, multidisciplinary project that seeks to harmonize data across the microbiome research community. We welcome any and all kinds of contributions. Our goal is to make it easy for you to contribute to the project, and to make sure that your contributions are properly reviewed and integrated.
"},{"location":"collaboration/#how-can-i-contribute","title":"How can I contribute?","text":"We welcome any and all kinds of contribution, including:
Please see our Contributing Guidelines for more information on how to contribute to the project, and our Code of Conduct for information on how to interact with the community.
"},{"location":"collaboration/#how-do-i-do-x-why-doesnt-y-work-where-can-i-go-to-get-help","title":"How do I do X? Why doesn\u2019t Y work? Where can I go to get help?","text":"First, please check if your question is answered on the FAQ and or in this documentation. We always welcome questions, bug reports, feature requests, and feedback via our GitHub issue tracker:
https://github.com/microbiomedata/nmdc-schema/issues
"},{"location":"collaboration/#how-do-i-run-a-collaborative-schema-project","title":"How do I run a collaborative schema project?","text":"Please check some guidelines from LinkML Schema Developers: https://linkml.io/linkml/howtos/collaborative-development.html Consult NMDC Schema Contribution guidelines directly: GoogleSlides
"},{"location":"collected_from/","title":"Slot: collected_from","text":"The Site from which a Biosample was collected
URI: nmdc:collected_from
"},{"location":"collected_from/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"collected_from/#properties","title":"Properties","text":"name: collected_from\ndescription: The Site from which a Biosample was collected\ntodos:\n- add an OBO slot_uri ?\ncomments:\n- this illustrates implementing a Biosample relation with a (binary) slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: collected_from\ndomain_of:\n- Biosample\nrange: FieldResearchSite\n\nURI: nmdc:collecting_biosamples_from_site_set
"},{"location":"collecting_biosamples_from_site_set/#inheritance","title":"Inheritance","text":"Range: CollectingBiosamplesFromSite
Multivalued: True
name: collecting_biosamples_from_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: collecting_biosamples_from_site_set\ndomain_of:\n- Database\nrange: CollectingBiosamplesFromSite\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant
URI: MIXS:0000011
"},{"location":"collection_date/#inheritance","title":"Inheritance","text":"name: collection_date\nannotations:\n expected_value:\n tag: expected_value\n value: date and time\ndescription: 'The time of sampling, either as an instance (single point in time) or\n interval. In case no exact time is available, the date/time can be right truncated\n i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\ntitle: collection date\nexamples:\n- value: 2018-05-11T10:00:00+01:00; 2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- collection date\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000011\nalias: collection_date\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nDate the incubation was harvested/collected/ended. Only relevant for incubation samples.
URI: nmdc:collection_date_inc
"},{"location":"collection_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_date_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_date_inc\ndescription: Date the incubation was harvested/collected/ended. Only relevant for\n incubation samples.\ntitle: incubation collection date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n all acceptable.\nexamples:\n- value: '2021-04-15'\n- value: 2021-04\n- value: '2021'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 2\nstring_serialization: '{date, arbitrary precision}'\nalias: collection_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nThe time of sampling, either as an instance (single point) or interval.
URI: nmdc:collection_time
"},{"location":"collection_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_time\ndescription: The time of sampling, either as an instance (single point) or interval.\ntitle: collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: '13:33'\n- value: '13:33:55'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 1\nstring_serialization: '{time, seconds optional}'\nalias: collection_time\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nTime the incubation was harvested/collected/ended. Only relevant for incubation samples.
URI: nmdc:collection_time_inc
"},{"location":"collection_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_time_inc\ndescription: Time the incubation was harvested/collected/ended. Only relevant for\n incubation samples.\ntitle: incubation collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: '13:33'\n- value: '13:33:55'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 3\nstring_serialization: '{time, seconds optional}'\nalias: collection_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nURI: nmdc:community
"},{"location":"community/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"community/#properties","title":"Properties","text":"name: community\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: community\ndomain_of:\n- Biosample\nrange: string\n\nEstimate of the completeness of the metagenome-assembled genome, estimated by a tool like CheckM.
URI: nmdc:completeness
"},{"location":"completeness/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"completeness/#properties","title":"Properties","text":"Range: Float
Minimum Value: 0
name: completeness\ndescription: Estimate of the completeness of the metagenome-assembled genome, estimated\n by a tool like CheckM.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completeness\ndomain_of:\n- EukEval\n- MagBin\nrange: float\nminimum_value: 0\n\nURI: nmdc:completion_date
"},{"location":"completion_date/#properties","title":"Properties","text":"name: completion_date\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completion_date\nrange: string\n\nIf provided, specifies the compression type
URI: nmdc:compression_type
"},{"location":"compression_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"compression_type/#properties","title":"Properties","text":"name: compression_type\ndescription: If provided, specifies the compression type\ntodos:\n- consider setting the range to an enum\nexamples:\n- value: gzip\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: compression_type\ndomain_of:\n- DataObject\nrange: string\n\nThe concentration of a substance used in a process
URI: nmdc:concentration
"},{"location":"concentration/#inheritance","title":"Inheritance","text":"name: concentration\ndescription: The concentration of a substance used in a process\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: concentration\nrange: QuantityValue\n\nPreliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized.
URI: nmdc:conditionings
"},{"location":"conditionings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"conditionings/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: conditionings\ndescription: Preliminary treatment of either phase with a suitable solution of the\n other phase (in the absence of main extractable solute(s)) so that when the subsequent\n equilibration is carried out changes in the (volume) phase ratio or in the concentrations\n of other components are minimized.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: conditionings\ndomain_of:\n- FiltrationProcess\nrange: string\nmultivalued: true\n\nElectrical conductivity of water
URI: MIXS:0000692
"},{"location":"conduc/#inheritance","title":"Inheritance","text":"name: conduc\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliSiemens per centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Electrical conductivity of water\ntitle: conductivity\nexamples:\n- value: 10 milliSiemens per centimeter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- conductivity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000692\nalias: conduc\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThis property links a database object to the set of configurations within it.
URI: nmdc:configuration_set
"},{"location":"configuration_set/#inheritance","title":"Inheritance","text":"Range: Configuration
Multivalued: True
name: configuration_set\ndescription: This property links a database object to the set of configurations within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: configuration_set\ndomain_of:\n- Database\nrange: Configuration\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA type of container.
URI: nmdc:contained_in
"},{"location":"contained_in/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot StorageProcess A planned process with the objective to preserve and protect material entitie... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no"},{"location":"contained_in/#properties","title":"Properties","text":"name: contained_in\ndescription: A type of container.\nexamples:\n- value: test tube\n- value: falcon tube\n- value: whirlpak\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contained_in\ndomain_of:\n- SubSamplingProcess\n- StorageProcess\nrange: ContainerCategoryEnum\n\nThe volume of the container an analyte is stored in or an activity takes place in
URI: nmdc:container_size
"},{"location":"container_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no FiltrationProcess The process of segregation of phases; e no"},{"location":"container_size/#properties","title":"Properties","text":"name: container_size\ndescription: The volume of the container an analyte is stored in or an activity takes\n place in\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: container_size\ndomain_of:\n- SubSamplingProcess\n- FiltrationProcess\nrange: QuantityValue\n\nEstimate of the completeness of the metagenome-assembled genome, estimated by a tool like CheckM.
URI: nmdc:contamination
"},{"location":"contamination/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"contamination/#properties","title":"Properties","text":"Range: Float
Minimum Value: 0
name: contamination\ndescription: Estimate of the completeness of the metagenome-assembled genome, estimated\n by a tool like CheckM.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contamination\ndomain_of:\n- EukEval\n- MagBin\nrange: float\nminimum_value: 0\n\nTotal size in bp of all contigs.
URI: nmdc:contig_bp
"},{"location":"contig_bp/#inheritance","title":"Inheritance","text":"name: contig_bp\ndescription: Total size in bp of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contig_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase
URI: nmdc:contigs
"},{"location":"contigs/#inheritance","title":"Inheritance","text":"name: contigs\ndescription: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contigs\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe cooling system identifier
URI: MIXS:0000785
"},{"location":"cool_syst_id/#inheritance","title":"Inheritance","text":"name: cool_syst_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The cooling system identifier\ntitle: cooling system identifier\nexamples:\n- value: '12345'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- cooling system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000785\nalias: cool_syst_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nbasic fields
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:core_field
"},{"location":"core_field/#inheritance","title":"Inheritance","text":"name: core field\ndescription: basic fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: core_field\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:count
"},{"location":"count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember yes"},{"location":"count/#properties","title":"Properties","text":"Range: Integer
Required: True
name: count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: count\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: integer\nrequired: true\n\nWhether or not crop is rotated, and if yes, rotation schedule
URI: MIXS:0000318
"},{"location":"crop_rotation/#inheritance","title":"Inheritance","text":"name: crop_rotation\nannotations:\n expected_value:\n tag: expected_value\n value: crop rotation status;schedule\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Whether or not crop is rotated, and if yes, rotation schedule\ntitle: history/crop rotation\nexamples:\n- value: yes;R2/2017-01-01/2018-12-31/P6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/crop rotation\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000318\nalias: crop_rotation\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nGiven a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.
URI: nmdc:ctg_l50
"},{"location":"ctg_l50/#inheritance","title":"Inheritance","text":"name: ctg_l50\ndescription: Given a set of contigs, the L50 is defined as the sequence length of\n the shortest contig at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.
URI: nmdc:ctg_l90
"},{"location":"ctg_l90/#inheritance","title":"Inheritance","text":"name: ctg_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n length for which the collection of all contigs of that length or longer contains\n at least 90% of the sum of the lengths of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum contig length.
URI: nmdc:ctg_logsum
"},{"location":"ctg_logsum/#inheritance","title":"Inheritance","text":"name: ctg_logsum\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum contig length.
URI: nmdc:ctg_max
"},{"location":"ctg_max/#inheritance","title":"Inheritance","text":"name: ctg_max\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.
URI: nmdc:ctg_n50
"},{"location":"ctg_n50/#inheritance","title":"Inheritance","text":"name: ctg_n50\ndescription: Given a set of contigs, each with its own length, the N50 count is defined\n as the smallest number_of_contigs whose length sum makes up half of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.
URI: nmdc:ctg_n90
"},{"location":"ctg_n90/#inheritance","title":"Inheritance","text":"name: ctg_n90\ndescription: Given a set of contigs, each with its own length, the N90 count is defined\n as the smallest number of contigs whose length sum makes up 90% of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nPowersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
URI: nmdc:ctg_powsum
"},{"location":"ctg_powsum/#inheritance","title":"Inheritance","text":"name: ctg_powsum\ndescription: Powersum of all contigs is the same as logsum except that it uses the\n sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nName or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.
URI: MIXS:0001041
"},{"location":"cult_root_med/#inheritance","title":"Inheritance","text":"name: cult_root_med\nannotations:\n expected_value:\n tag: expected_value\n value: name, PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name or reference for the hydroponic or in vitro culture rooting medium;\n can be the name of a commonly used medium or reference to a specific medium, e.g.\n Murashige and Skoog medium. If the medium has not been formally published, use the\n rooting medium descriptors.\ntitle: culture rooting medium\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- culture rooting medium\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001041\nalias: cult_root_med\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nPresent state of sample site
URI: MIXS:0001080
"},{"location":"cur_land_use/#inheritance","title":"Inheritance","text":"name: cur_land_use\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Present state of sample site\ntitle: current land use\nexamples:\n- value: conifers\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current land use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001080\nalias: cur_land_use\ndomain_of:\n- Biosample\nrange: cur_land_use_enum\nmultivalued: false\n\nVegetation classification from one or more standard classification systems, or agricultural crop
URI: MIXS:0000312
"},{"location":"cur_vegetation/#inheritance","title":"Inheritance","text":"name: cur_vegetation\nannotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Vegetation classification from one or more standard classification systems,\n or agricultural crop\ntitle: current vegetation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000312\nalias: cur_vegetation\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\nReference or method used in vegetation classification
URI: MIXS:0000314
"},{"location":"cur_vegetation_meth/#inheritance","title":"Inheritance","text":"name: cur_vegetation_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in vegetation classification\ntitle: current vegetation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000314\nalias: cur_vegetation_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe category of the file, such as instrument data from data generation or processed data from a workflow execution.
URI: nmdc:data_category
"},{"location":"data_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_category/#properties","title":"Properties","text":"name: data_category\ndescription: The category of the file, such as instrument data from data generation\n or processed data from a workflow execution.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: data_category\ndomain_of:\n- DataObject\nrange: DataCategoryEnum\n\nThis property links a database object to the set of data generations within it.
URI: nmdc:data_generation_set
"},{"location":"data_generation_set/#inheritance","title":"Inheritance","text":"Range: DataGeneration
Multivalued: True
name: data_generation_set\ndescription: This property links a database object to the set of data generations\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: data_generation_set\ndomain_of:\n- Database\nrange: DataGeneration\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of data objects within it.
URI: nmdc:data_object_set
"},{"location":"data_object_set/#inheritance","title":"Inheritance","text":"Range: DataObject
Multivalued: True
name: data_object_set\ndescription: This property links a database object to the set of data objects within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: data_object_set\ndomain_of:\n- Database\nrange: DataObject\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe type of file represented by the data object.
URI: nmdc:data_object_type
"},{"location":"data_object_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_object_type/#properties","title":"Properties","text":"name: data_object_type\ndescription: The type of file represented by the data object.\nexamples:\n- value: FT ICR-MS Analysis Results\n- value: GC-MS Metabolomics Results\nfrom_schema: https://w3id.org/nmdc/nmdc\nstructured_aliases:\n data_object_type:\n literal_form: data_object_type\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\nrank: 1000\nalias: data_object_type\ndomain_of:\n- DataObject\nrange: FileTypeEnum\n\nfrom database class
URI: nmdc:date_created
"},{"location":"date_created/#properties","title":"Properties","text":"name: date_created\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: date_created\nrange: string\n\nThe date of the last time it rained
URI: MIXS:0000786
"},{"location":"date_last_rain/#inheritance","title":"Inheritance","text":"name: date_last_rain\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The date of the last time it rained\ntitle: date last rain\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- date last rain\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000786\nalias: date_last_rain\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nThe definition of the ontology term as provided by the ontology.
URI: nmdc:definition
"},{"location":"definition/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EnvironmentalMaterialTerm no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no OrthologyGroup A set of genes or gene products in which all members are orthologous no OntologyClass A representation of class defined in an external ontology no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"definition/#properties","title":"Properties","text":"name: definition\ndescription: The definition of the ontology term as provided by the ontology.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: definition\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: string\n\nDensity of the sample, which is its mass per unit volume (aka volumetric mass density)
URI: MIXS:0000435
"},{"location":"density/#inheritance","title":"Inheritance","text":"name: density\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter, gram per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Density of the sample, which is its mass per unit volume (aka volumetric\n mass density)\ntitle: density\nexamples:\n- value: 1000 kilogram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000435\nalias: density\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMain depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000992
"},{"location":"depos_env/#inheritance","title":"Inheritance","text":"name: depos_env\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: depositional environment\nexamples:\n- value: Continental - Alluvial\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000992\nalias: depos_env\ndomain_of:\n- Biosample\nrange: depos_env_enum\nmultivalued: false\n\nThe vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.
URI: MIXS:0000018
"},{"location":"depth/#inheritance","title":"Inheritance","text":"name: depth\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: The vertical distance below local surface, e.g. for sediment or soil\n samples depth is measured from sediment or soil surface, respectively. Depth can\n be reported as an interval for subsurface samples.\ntitle: depth\nexamples:\n- value: 10 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000018\nalias: depth\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\na human-readable description of a thing
URI: dcterms:description
"},{"location":"description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Manifest A qualified collection of DataObjects that can be analyzed together in the sa... no OrthologyGroup A set of genes or gene products in which all members are orthologous no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no MaterialEntity no ProcessedSample no NamedThing a databased entity or concept/class no Configuration A set of parameters that define the actions of a process and is shared among ... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no GeneProduct A molecule encoded by a gene that has an evolved function no MetatranscriptomeAnnotation no EnvironmentalMaterialTerm no NomAnalysis no ImageValue An attribute value representing an image no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Study A study summarizes the overall goal of a research initiative and outlines the... yes CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no OntologyClass A representation of class defined in an external ontology no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no CalibrationInformation A calibration object that is associated with a process no LibraryPreparation no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no MetatranscriptomeAssembly no Biosample Biological source material which can be characterized by an experiment no WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no DataObject An object that primarily consists of symbols that represent information yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no Instrument A material entity that is designed to perform a function in a scientific inve... no ProtocolExecution A PlannedProces that has PlannedProcess parts no Sample A sample is a material entity that can be characterized by an experiment no Site no MetaproteomicsAnalysis no PlannedProcess no"},{"location":"description/#properties","title":"Properties","text":"name: description\ndescription: a human-readable description of a thing\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: dcterms:description\nalias: description\ndomain_of:\n- ImageValue\n- NamedThing\nrange: string\n\nSome frequently asked questions about developing the NMDC Schema.
"},{"location":"developer-docs/#what-are-some-effective-strategies-for-collaborative-schema-development","title":"What are some effective strategies for collaborative schema development?","text":"LinkML Collaborative Development Google Slides Presentation
"},{"location":"developer-docs/#how-do-i-migrate-from-one-version-of-the-nmdc-schema-to-another","title":"How do I migrate from one version of the NMDC schema to another?","text":"Version 10 to 11 migration
"},{"location":"developer-docs/#how-do-i-view-the-nmdc-schema-programmatically","title":"How do I view the NMDC schema programmatically?","text":"NMDC SchemaView Documentation SchemaView Documentation
"},{"location":"dew_point/","title":"Slot: dew point (dew_point)","text":"The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.
URI: MIXS:0000129
"},{"location":"dew_point/#inheritance","title":"Inheritance","text":"name: dew_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The temperature to which a given parcel of humid air must be cooled,\n at constant barometric pressure, for water vapor to condense into water.\ntitle: dew point\nexamples:\n- value: 22 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000129\nalias: dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of diether lipids; can include multiple types of diether lipids
URI: MIXS:0000178
"},{"location":"diether_lipids/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: diether_lipids\nannotations:\n expected_value:\n tag: expected_value\n value: diether lipid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of diether lipids; can include multiple types of diether\n lipids\ntitle: diether lipids\nexamples:\n- value: 0.2 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- diether lipids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000178\nalias: diether_lipids\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nWhen rendering information, this attribute to specify the order in which the information should be rendered.
URI: nmdc:display_order
"},{"location":"display_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ImageValue An attribute value representing an image no"},{"location":"display_order/#properties","title":"Properties","text":"name: display_order\ndescription: When rendering information, this attribute to specify the order in which\n the information should be rendered.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: display_order\ndomain_of:\n- ImageValue\nrange: integer\n\nConcentration of dissolved carbon dioxide in the sample or liquid portion of the sample
URI: MIXS:0000436
"},{"location":"diss_carb_dioxide/#inheritance","title":"Inheritance","text":"name: diss_carb_dioxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved carbon dioxide in the sample or liquid portion\n of the sample\ntitle: dissolved carbon dioxide\nexamples:\n- value: 5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000436\nalias: diss_carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved hydrogen
URI: MIXS:0000179
"},{"location":"diss_hydrogen/#inheritance","title":"Inheritance","text":"name: diss_hydrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved hydrogen\ntitle: dissolved hydrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved hydrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000179\nalias: diss_hydrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter
URI: MIXS:0000434
"},{"location":"diss_inorg_carb/#inheritance","title":"Inheritance","text":"name: diss_inorg_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Dissolved inorganic carbon concentration in the sample, typically measured\n after filtering the sample using a 0.45 micrometer filter\ntitle: dissolved inorganic carbon\nexamples:\n- value: 2059 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000434\nalias: diss_inorg_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved inorganic nitrogen
URI: MIXS:0000698
"},{"location":"diss_inorg_nitro/#inheritance","title":"Inheritance","text":"name: diss_inorg_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved inorganic nitrogen\ntitle: dissolved inorganic nitrogen\nexamples:\n- value: 761 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000698\nalias: diss_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved inorganic phosphorus in the sample
URI: MIXS:0000106
"},{"location":"diss_inorg_phosp/#inheritance","title":"Inheritance","text":"name: diss_inorg_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved inorganic phosphorus in the sample\ntitle: dissolved inorganic phosphorus\nexamples:\n- value: 56.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000106\nalias: diss_inorg_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved iron in the sample
URI: MIXS:0000139
"},{"location":"diss_iron/#inheritance","title":"Inheritance","text":"name: diss_iron\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved iron in the sample\ntitle: dissolved iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000139\nalias: diss_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid
URI: MIXS:0000433
"},{"location":"diss_org_carb/#inheritance","title":"Inheritance","text":"name: diss_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved organic carbon in the sample, liquid portion\n of the sample, or aqueous phase of the fluid\ntitle: dissolved organic carbon\nexamples:\n- value: 197 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000433\nalias: diss_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
URI: MIXS:0000162
"},{"location":"diss_org_nitro/#inheritance","title":"Inheritance","text":"name: diss_org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Dissolved organic nitrogen concentration measured as; total dissolved\n nitrogen - NH4 - NO3 - NO2\ntitle: dissolved organic nitrogen\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000162\nalias: diss_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved oxygen
URI: MIXS:0000119
"},{"location":"diss_oxygen/#inheritance","title":"Inheritance","text":"name: diss_oxygen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved oxygen\ntitle: dissolved oxygen\nexamples:\n- value: 175 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000119\nalias: diss_oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).
URI: MIXS:0000438
"},{"location":"diss_oxygen_fluid/#inheritance","title":"Inheritance","text":"name: diss_oxygen_fluid\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved oxygen in the oil field produced fluids as\n it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\ntitle: dissolved oxygen in fluids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen in fluids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000438\nalias: diss_oxygen_fluid\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n260/280 measurement of DNA sample purity
URI: nmdc:dna_absorb1
"},{"location":"dna_absorb1/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: dna_absorb1\ndescription: 260/280 measurement of DNA sample purity\ntitle: DNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nis_a: biomaterial_purity\nalias: dna_absorb1\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\n260/230 measurement of DNA sample purity
URI: nmdc:dna_absorb2
"},{"location":"dna_absorb2/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: dna_absorb2\ndescription: 260/230 measurement of DNA sample purity\ntitle: DNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nis_a: biomaterial_purity\nalias: dna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\nProvide information on the site your DNA sample was collected from
URI: nmdc:dna_collect_site
"},{"location":"dna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_collect_site/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_collect_site\ndescription: Provide information on the site your DNA sample was collected from\ntitle: DNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: dna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_concentration
"},{"location":"dna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProcessedSample no Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_concentration/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 2000
name: dna_concentration\ntitle: DNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nalias: dna_concentration\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\nTube or plate (96-well)
URI: nmdc:dna_cont_type
"},{"location":"dna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_type/#properties","title":"Properties","text":"Range: JgiContTypeEnum
Recommended: True
name: dna_cont_type\ndescription: Tube or plate (96-well)\ntitle: DNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: dna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: JgiContTypeEnum\nrecommended: true\n\nURI: nmdc:dna_cont_well
"},{"location":"dna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_well/#properties","title":"Properties","text":"Range: String
Recommended: True
Regex pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
name: dna_cont_well\ntitle: DNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: dna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\npattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n\nURI: nmdc:dna_container_id
"},{"location":"dna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_container_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_container_id\ntitle: DNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: dna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_dnase
"},{"location":"dna_dnase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_dnase/#properties","title":"Properties","text":"Range: YesNoEnum
Recommended: True
name: dna_dnase\ntitle: DNase treatment DNA\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nalias: dna_dnase\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: YesNoEnum\nrecommended: true\n\nDescribe the method/protocol/kit used to extract DNA/RNA.
URI: nmdc:dna_isolate_meth
"},{"location":"dna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_isolate_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: DNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Sample Isolation Method\nrank: 16\nstring_serialization: '{text}'\nalias: dna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nList any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.
URI: nmdc:dna_organisms
"},{"location":"dna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_organisms/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\ntitle: DNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: dna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_project_contact
"},{"location":"dna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_project_contact/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_project_contact\ntitle: DNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: dna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_samp_id
"},{"location":"dna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_samp_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_samp_id\ntitle: DNA sample ID\ntodos:\n- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n have two identifiers. How to force uniqueness? Moot because that column will be\n prefilled?\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: dna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nSolution in which the DNA sample has been suspended
URI: nmdc:dna_sample_format
"},{"location":"dna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_format/#properties","title":"Properties","text":"Range: DNASampleFormatEnum
Recommended: True
name: dna_sample_format\ndescription: Solution in which the DNA sample has been suspended\ntitle: DNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: dna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: DNASampleFormatEnum\nrecommended: true\n\nGive the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
URI: nmdc:dna_sample_name
"},{"location":"dna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_sample_name\ndescription: Give the DNA sample a name that is meaningful to you. Sample names must\n be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: DNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: dna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project
"},{"location":"dna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project\ntitle: DNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Seq Project ID\nrank: 1\nstring_serialization: '{text}'\nalias: dna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project_name
"},{"location":"dna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project_name\ntitle: DNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: JGI Pond metagenomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: dna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project_pi
"},{"location":"dna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_pi/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project_pi\ntitle: DNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: dna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_volume
"},{"location":"dna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_volume/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: dna_volume\ntitle: DNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n accepts values < 25, but JGI may refuse to process them unless permission has been\n granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: dna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nURI: nmdc:dnase_rna
"},{"location":"dnase_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dnase_rna/#properties","title":"Properties","text":"Range: YesNoEnum
Recommended: True
name: dnase_rna\ntitle: DNase treated\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Was Sample DNAse treated?\nrank: 13\nalias: dnase_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: YesNoEnum\nrecommended: true\n\nThe resource type the corresponding doi resolves to.
URI: nmdc:doi_category
"},{"location":"doi_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_category/#properties","title":"Properties","text":"Range: DoiCategoryEnum
Required: True
name: doi_category\ndescription: The resource type the corresponding doi resolves to.\nexamples:\n- value: dataset_doi\n description: The corresponding DOI is a dataset resource type.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: doi_category\ndomain_of:\n- Doi\nrange: DoiCategoryEnum\nrequired: true\n\nThe authority, or organization, the DOI is associated with.
URI: nmdc:doi_provider
"},{"location":"doi_provider/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_provider/#properties","title":"Properties","text":"name: doi_provider\ndescription: The authority, or organization, the DOI is associated with.\nexamples:\n- value: ess_dive\n description: The corresponding DOI is associated with ESS-DIVE.\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C74932\nrank: 1000\nalias: doi_provider\ndomain_of:\n- Doi\nrange: DoiProviderEnum\n\nA digital object identifier, which is intended to persistantly identify some resource on the web.
URI: nmdc:doi_value
"},{"location":"doi_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_value/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: doi_value\ndescription: A digital object identifier, which is intended to persistantly identify\n some resource on the web.\nexamples:\n- value: doi:10.46936/10.25585/60000880\n description: The DOI links to an electronic document.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOI\n- digital object identifier\nexact_mappings:\n- OBI:0002110\nnarrow_mappings:\n- edam.data:1188\nrank: 1000\nalias: doi_value\ndomain_of:\n- Doi\nrange: uriorcurie\nrequired: true\npattern: ^doi:10.\\d{2,9}/.*$\n\nThe composite type of the door
URI: MIXS:0000795
"},{"location":"door_comp_type/#inheritance","title":"Inheritance","text":"name: door_comp_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The composite type of the door\ntitle: door type, composite\nexamples:\n- value: revolving\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, composite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000795\nalias: door_comp_type\ndomain_of:\n- Biosample\nrange: door_comp_type_enum\nmultivalued: false\n\nThe phsical condition of the door
URI: MIXS:0000788
"},{"location":"door_cond/#inheritance","title":"Inheritance","text":"name: door_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The phsical condition of the door\ntitle: door condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000788\nalias: door_cond\ndomain_of:\n- Biosample\nrange: door_cond_enum\nmultivalued: false\n\nThe direction the door opens
URI: MIXS:0000789
"},{"location":"door_direct/#inheritance","title":"Inheritance","text":"name: door_direct\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The direction the door opens\ntitle: door direction of opening\nexamples:\n- value: inward\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door direction of opening\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000789\nalias: door_direct\ndomain_of:\n- Biosample\nrange: door_direct_enum\nmultivalued: false\n\nThe relative location of the door in the room
URI: MIXS:0000790
"},{"location":"door_loc/#inheritance","title":"Inheritance","text":"name: door_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the door in the room\ntitle: door location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000790\nalias: door_loc\ndomain_of:\n- Biosample\nrange: door_loc_enum\nmultivalued: false\n\nThe material the door is composed of
URI: MIXS:0000791
"},{"location":"door_mat/#inheritance","title":"Inheritance","text":"name: door_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material the door is composed of\ntitle: door material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000791\nalias: door_mat\ndomain_of:\n- Biosample\nrange: door_mat_enum\nmultivalued: false\n\nThe type of movement of the door
URI: MIXS:0000792
"},{"location":"door_move/#inheritance","title":"Inheritance","text":"name: door_move\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of movement of the door\ntitle: door movement\nexamples:\n- value: swinging\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door movement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000792\nalias: door_move\ndomain_of:\n- Biosample\nrange: door_move_enum\nmultivalued: false\n\nThe size of the door
URI: MIXS:0000158
"},{"location":"door_size/#inheritance","title":"Inheritance","text":"name: door_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The size of the door\ntitle: door area or size\nexamples:\n- value: 2.5 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door area or size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000158\nalias: door_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of door material
URI: MIXS:0000794
"},{"location":"door_type/#inheritance","title":"Inheritance","text":"name: door_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of door material\ntitle: door type\nexamples:\n- value: wooden\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000794\nalias: door_type\ndomain_of:\n- Biosample\nrange: door_type_enum\nmultivalued: false\n\nThe type of metal door
URI: MIXS:0000796
"},{"location":"door_type_metal/#inheritance","title":"Inheritance","text":"name: door_type_metal\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of metal door\ntitle: door type, metal\nexamples:\n- value: hollow\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, metal\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000796\nalias: door_type_metal\ndomain_of:\n- Biosample\nrange: door_type_metal_enum\nmultivalued: false\n\nThe type of wood door
URI: MIXS:0000797
"},{"location":"door_type_wood/#inheritance","title":"Inheritance","text":"name: door_type_wood\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of wood door\ntitle: door type, wood\nexamples:\n- value: battened\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, wood\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000797\nalias: door_type_wood\ndomain_of:\n- Biosample\nrange: door_type_wood_enum\nmultivalued: false\n\nSigns of the presence of mold or mildew on a door
URI: MIXS:0000793
"},{"location":"door_water_mold/#inheritance","title":"Inheritance","text":"name: door_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on a door\ntitle: door signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000793\nalias: door_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nVisible waveband radiance and irradiance measurements in the water column
URI: MIXS:0000703
"},{"location":"down_par/#inheritance","title":"Inheritance","text":"name: down_par\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microEinstein per square meter per second, microEinstein per square centimeter\n per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Visible waveband radiance and irradiance measurements in the water column\ntitle: downward PAR\nexamples:\n- value: 28.71 microEinstein per square meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- downward PAR\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000703\nalias: down_par\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDrainage classification from a standard system such as the USDA system
URI: MIXS:0001085
"},{"location":"drainage_class/#inheritance","title":"Inheritance","text":"name: drainage_class\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Drainage classification from a standard system such as the USDA system\ntitle: drainage classification\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drainage classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001085\nalias: drainage_class\ndomain_of:\n- Biosample\nrange: drainage_class_enum\nmultivalued: false\n\nThe buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents
URI: MIXS:0000798
"},{"location":"drawings/#inheritance","title":"Inheritance","text":"name: drawings\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The buildings architectural drawings; if design is chosen, indicate phase-conceptual,\n schematic, design development, and construction documents\ntitle: drawings\nexamples:\n- value: sketch\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drawings\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000798\nalias: drawings\ndomain_of:\n- Biosample\nrange: drawings_enum\nmultivalued: false\n\nThe elapsed time of an activity.
URI: nmdc:duration
"},{"location":"duration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no"},{"location":"duration/#properties","title":"Properties","text":"name: duration\ndescription: The elapsed time of an activity.\nexamples:\n- value: JsonObj(has_numeric_value=2, has_unit='hours')\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: duration\ndomain_of:\n- MixingProcess\n- DissolvingProcess\n- ChemicalConversionProcess\n- MobilePhaseSegment\nrange: QuantityValue\n\nAn ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.
URI: nmdc:ecosystem
"},{"location":"ecosystem/#inheritance","title":"Inheritance","text":"name: ecosystem\ndescription: An ecosystem is a combination of a physical environment (abiotic factors)\n and all the organisms (biotic factors) that interact with this environment. Ecosystem\n is in position 1/5 in a GOLD path.\ncomments:\n- The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism or environmental\n sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated,\n and Engineered. They represent samples collected from a natural environment or from\n another organism or from engineered environments like bioreactors respectively.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nEcosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.
URI: nmdc:ecosystem_category
"},{"location":"ecosystem_category/#inheritance","title":"Inheritance","text":"name: ecosystem_category\ndescription: Ecosystem categories represent divisions within the ecosystem based on\n specific characteristics of the environment from where an organism or sample is\n isolated. Ecosystem category is in position 2/5 in a GOLD path.\ncomments:\n- The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or phyla\n and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_category\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nA unique id representing the GOLD classifiers associated with a sample.
URI: nmdc:ecosystem_path_id
"},{"location":"ecosystem_path_id/#properties","title":"Properties","text":"name: ecosystem_path_id\ndescription: A unique id representing the GOLD classifiers associated with a sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ecosystem_path_id\nrange: string\n\nEcosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.
URI: nmdc:ecosystem_subtype
"},{"location":"ecosystem_subtype/#inheritance","title":"Inheritance","text":"name: ecosystem_subtype\ndescription: Ecosystem subtypes represent further subdivision of Ecosystem types into\n more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.\ncomments:\n- Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for\n example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem\n subtype category.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_subtype\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nEcosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.
URI: nmdc:ecosystem_type
"},{"location":"ecosystem_type/#inheritance","title":"Inheritance","text":"name: ecosystem_type\ndescription: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still broad\n but specific to the characteristics of a given environment. Ecosystem type is in\n position 3/5 in a GOLD path.\ncomments:\n- The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air\n as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_type\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nPercentage of volatile solids removed from the anaerobic digestor
URI: MIXS:0000657
"},{"location":"efficiency_percent/#inheritance","title":"Inheritance","text":"name: efficiency_percent\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Percentage of volatile solids removed from the anaerobic digestor\ntitle: efficiency percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- efficiency percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000657\nalias: efficiency_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nElevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.
URI: MIXS:0000093
"},{"location":"elev/#inheritance","title":"Inheritance","text":"name: elev\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the surface,\n such as an aircraft in flight or a spacecraft in orbit.\ntitle: elevation\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevation\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000093\nalias: elev\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: float\nmultivalued: false\n\nThe number of elevators within the built structure
URI: MIXS:0000799
"},{"location":"elevator/#inheritance","title":"Inheritance","text":"name: elevator\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of elevators within the built structure\ntitle: elevator count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000799\nalias: elevator\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA high-level categorization for how the processed sample is introduced into a mass spectrometer.
URI: nmdc:eluent_introduction_category
"},{"location":"eluent_introduction_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"eluent_introduction_category/#properties","title":"Properties","text":"name: eluent_introduction_category\ndescription: A high-level categorization for how the processed sample is introduced\n into a mass spectrometer.\nexamples:\n- value: liquid_chromatography\n- value: direct_infusion_syringe\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: eluent_introduction_category\ndomain_of:\n- MassSpectrometry\nrange: EluentIntroductionCategoryEnum\n\nAn email address for an entity such as a person. This should be the primary email address used.
URI: schema:email
"},{"location":"email/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"email/#properties","title":"Properties","text":"name: email\ndescription: An email address for an entity such as a person. This should be the primary\n email address used.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: schema:email\nalias: email\ndomain_of:\n- PersonValue\nrange: string\n\nIf true, the data are embargoed and not available for public access.
URI: nmdc:embargoed
"},{"location":"embargoed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"embargoed/#properties","title":"Properties","text":"Range: Boolean
Recommended: True
name: embargoed\ndescription: If true, the data are embargoed and not available for public access.\ntodos:\n- make this required?\n- first apply to Biosample\n- try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n- applying to a Study may not be granular enough\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: embargoed\ndomain_of:\n- Biosample\nrange: boolean\nrecommended: true\n\nA list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.
URI: nmdc:emsl_biosample_identifiers
"},{"location":"emsl_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: emsl_biosample_identifiers\ndescription: A list of identifiers for the biosample from the EMSL database. This\n is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n EMSL NEXUS database.\ntitle: EMSL Biosample Identifiers\ntodos:\n- removed \"planned\" once NEXUS is online\n- determine real expansion for emsl prefix\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- emsl_identifiers\nalias: emsl_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:emsl_identifiers
"},{"location":"emsl_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain emsl_project_identifiers Identifiers that link a NMDC study to the EMSL user facility website hosting ... None Study emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database None Biosample"},{"location":"emsl_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: emsl_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: emsl_identifiers\nrange: string\n\nIdentifiers that link a NMDC study to the EMSL user facility website hosting the project description of an EMSL user project
URI: nmdc:emsl_project_identifiers
"},{"location":"emsl_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^emsl\\.project:[0-9]{5}$
name: emsl_project_identifiers\ndescription: Identifiers that link a NMDC study to the EMSL user facility website\n hosting the project description of an EMSL user project\ntitle: EMSL Project Identifiers\ntodos:\n- elaborate on description\nnotes:\n- these identifiers are all currently 5 digits long but that could change in the future\nexamples:\n- value: emsl.project:60141\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-schema/issues/927#issuecomment-1802136437\nrank: 1000\nis_a: study_identifiers\nmixins:\n- emsl_identifiers\nalias: emsl_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^emsl\\.project:[0-9]{5}$\n\nThe temperature at which the sample should be stored upon delivery to EMSL
URI: nmdc:emsl_store_temp
"},{"location":"emsl_store_temp/#properties","title":"Properties","text":"Range: String
Recommended: True
name: emsl_store_temp\ndescription: The temperature at which the sample should be stored upon delivery to\n EMSL\ntitle: EMSL sample storage temperature, deg. C\ntodos:\n- add 'see_alsos' with link to NEXUS info\ncomments:\n- Enter a temperature in celsius. Numeric portion only.\nexamples:\n- value: '-80'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{float}'\nalias: emsl_store_temp\nslot_group: EMSL\nrange: string\nrecommended: true\n\nAmount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types
URI: MIXS:0000660
"},{"location":"emulsions/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: emulsions\nannotations:\n expected_value:\n tag: expected_value\n value: emulsion name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount or concentration of substances such as paints, adhesives, mayonnaise,\n hair colorants, emulsified oils, etc.; can include multiple emulsion types\ntitle: emulsions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- emulsions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000660\nalias: emulsions\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA
URI: nmdc:encodes
"},{"location":"encodes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"encodes/#properties","title":"Properties","text":"name: encodes\ndescription: The gene product encoded by this feature. Typically this is used for\n a CDS feature or gene feature which will encode a protein. It can also be used by\n a nc transcript ot gene feature that encoded a ncRNA\ntodos:\n- If we revert Reaction back into the schema, that would be a reasonable domain for\n this slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: encodes\ndomain_of:\n- GenomeFeature\nrange: GeneProduct\n\nThe end of the feature in positive 1-based integer coordinates
URI: nmdc:end
"},{"location":"end/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: end\ndescription: The end of the feature in positive 1-based integer coordinates\ncomments:\n- '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n feature, end = the position of the end + the length of the landmark feature.\"'\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:end_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: end\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\nThe date on which any process or activity was ended
URI: nmdc:end_date
"},{"location":"end_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAnnotation no NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no LibraryPreparation no StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ProtocolExecution A PlannedProces that has PlannedProcess parts no MetaproteomicsAnalysis no PlannedProcess no"},{"location":"end_date/#properties","title":"Properties","text":"name: end_date\ndescription: The date on which any process or activity was ended\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: end_date\ndomain_of:\n- PlannedProcess\nrange: string\n\nURI: nmdc:ended_at_time
"},{"location":"ended_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NomAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAnnotation no MetaproteomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"ended_at_time/#properties","title":"Properties","text":"Range: String
Regex pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$
name: ended_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:endedAtTime\nrank: 1000\nalias: ended_at_time\ndomain_of:\n- WorkflowExecution\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\nReport the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
URI: MIXS:0000012
"},{"location":"env_broad_scale/#inheritance","title":"Inheritance","text":"name: env_broad_scale\nannotations:\n expected_value:\n tag: expected_value\n value: The major environment type(s) where the sample was collected. Recommend\n subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one\n or more pipes.\n tooltip:\n tag: tooltip\n value: The biome or major environmental system where the sample or specimen originated.\n Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment\n Ontology (ENVO). For host-associated or plant-associated samples, use terms\n from the UBERON or Plant Ontology to describe the broad anatomical or morphological\n context\ndescription: 'Report the major environmental system the sample or specimen came from.\n The system(s) identified should have a coarse spatial grain, to provide the general\n environmental context of where the sampling was done (e.g. in the desert or a rainforest).\n We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\n EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\ntitle: broad-scale environmental context\nexamples:\n- value: oceanic epipelagic zone biome [ENVO:01000035]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- broad-scale environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000012\nalias: env_broad_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nReport the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.
URI: MIXS:0000013
"},{"location":"env_local_scale/#inheritance","title":"Inheritance","text":"name: env_local_scale\nannotations:\n expected_value:\n tag: expected_value\n value: Environmental entities having causal influences upon the entity at time\n of sampling.\n tooltip:\n tag: tooltip\n value: The specific environmental entities or features near the sample or specimen\n that significantly influence its characteristics or composition. These entities\n are typically smaller in scale than the broad environmental context. Values\n for this field should be countable, material nouns and must be chosen from subclasses\n of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO).\n For host-associated or plant-associated samples, use terms from the UBERON or\n Plant Ontology to describe specific anatomical structures or plant parts.\ndescription: 'Report the entity or entities which are in the sample or specimen\u2019s\n local vicinity and which you believe have significant causal influences on your\n sample or specimen. We recommend using EnvO terms which are of smaller spatial grain\n than your entry for env_broad_scale. Terms, such as anatomical sites, from other\n OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in\n this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\ntitle: local environmental context\nexamples:\n- value: litter layer [ENVO:01000338]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- local environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000013\nalias: env_local_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nReport the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).
URI: MIXS:0000014
"},{"location":"env_medium/#inheritance","title":"Inheritance","text":"name: env_medium\nannotations:\n expected_value:\n tag: expected_value\n value: The material displaced by the entity at time of sampling. Recommend subclasses\n of environmental material [ENVO:00010483].\n tooltip:\n tag: tooltip\n value: The predominant environmental material or substrate that directly surrounds\n or hosts the sample or specimen at the time of sampling. Choose values from\n subclasses of the 'environmental material' class [ENVO:00010483] in the Environment\n Ontology (ENVO). Values for this field should be measurable or mass material\n nouns, representing continuous environmental materials. For host-associated\n or plant-associated samples, use terms from the UBERON or Plant Ontology to\n indicate a tissue, organ, or plant structure\ndescription: 'Report the environmental material(s) immediately surrounding the sample\n or specimen at the time of sampling. We recommend using subclasses of ''environmental\n material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about\n how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n . Terms from other OBO ontologies are permissible as long as they reference mass/volume\n nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree,\n a leaf, a table top).'\ntitle: environmental medium\nexamples:\n- value: soil [ENVO:00001998]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental medium\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000014\nalias: env_medium\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nMIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
URI: nmdc:env_package
"},{"location":"env_package/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"env_package/#properties","title":"Properties","text":"name: env_package\ndescription: MIxS extension for reporting of measurements and observations obtained\n from one or more of the environments where the sample was obtained. All environmental\n packages listed here are further defined in separate subtables. By giving the name\n of the environmental package, a selection of fields can be made from the subtables\n and can be reported\nnotes:\n- no longer in MIxS as of 6.0?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental package\nrank: 1000\nalias: env_package\ndomain_of:\n- Biosample\nrange: TextValue\n\nfield describing environmental aspect of a sample
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:environment_field
"},{"location":"environment_field/#inheritance","title":"Inheritance","text":"name: environment field\ndescription: field describing environmental aspect of a sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: environment_field\ndomain_of:\n- Biosample\nrange: string\n\nThe number of escalators within the built structure
URI: MIXS:0000800
"},{"location":"escalator/#inheritance","title":"Inheritance","text":"name: escalator\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of escalators within the built structure\ntitle: escalator count\nexamples:\n- value: '4'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- escalator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000800\nalias: escalator\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of ethylbenzene in the sample
URI: MIXS:0000155
"},{"location":"ethylbenzene/#inheritance","title":"Inheritance","text":"name: ethylbenzene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ethylbenzene in the sample\ntitle: ethylbenzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ethylbenzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000155\nalias: ethylbenzene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nfrom database class
URI: nmdc:etl_software_version
"},{"location":"etl_software_version/#properties","title":"Properties","text":"name: etl_software_version\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: etl_software_version\nrange: string\n\nContains results from evaluating if a Metagenome-Assembled Genome is of eukaryotic lineage.
URI: nmdc:eukaryotic_evaluation
"},{"location":"eukaryotic_evaluation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"eukaryotic_evaluation/#properties","title":"Properties","text":"name: eukaryotic_evaluation\ndescription: Contains results from evaluating if a Metagenome-Assembled Genome is\n of eukaryotic lineage.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: eukaryotic_evaluation\ndomain_of:\n- MagBin\nrange: EukEval\n\nThe computing resource or facility where the workflow was executed.
URI: nmdc:execution_resource
"},{"location":"execution_resource/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NomAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAnnotation no MetaproteomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow yes"},{"location":"execution_resource/#properties","title":"Properties","text":"name: execution_resource\ndescription: The computing resource or facility where the workflow was executed.\nexamples:\n- value: NERSC-Cori\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: execution_resource\ndomain_of:\n- WorkflowExecution\nrange: ExecutionResourceEnum\n\nThe amount of exposed ductwork in the room
URI: MIXS:0000144
"},{"location":"exp_duct/#inheritance","title":"Inheritance","text":"name: exp_duct\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The amount of exposed ductwork in the room\ntitle: exposed ductwork\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed ductwork\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000144\nalias: exp_duct\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of exposed pipes in the room
URI: MIXS:0000220
"},{"location":"exp_pipe/#inheritance","title":"Inheritance","text":"name: exp_pipe\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of exposed pipes in the room\ntitle: exposed pipes\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed pipes\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000220\nalias: exp_pipe\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nExperimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
URI: MIXS:0000008
"},{"location":"experimental_factor/#inheritance","title":"Inheritance","text":"name: experimental_factor\nannotations:\n expected_value:\n tag: expected_value\n value: text or EFO and/or OBI\ndescription: Experimental factors are essentially the variable aspects of an experiment\n design which can be used to describe an experiment, or set of experiments, in an\n increasingly detailed manner. This field accepts ontology terms from Experimental\n Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a\n browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\ntitle: experimental factor\nexamples:\n- value: time series design [EFO:EFO_0001779]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- experimental factor\nrank: 1000\nis_a: investigation field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000008\nalias: experimental_factor\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nOther details about your sample that you feel can't be accurately represented in the available columns.
URI: nmdc:experimental_factor_other
"},{"location":"experimental_factor_other/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"experimental_factor_other/#properties","title":"Properties","text":"Range: String
Recommended: True
name: experimental_factor_other\ndescription: Other details about your sample that you feel can't be accurately represented\n in the available columns.\ntitle: experimental factor- other\ncomments:\n- This slot accepts open-ended text about your sample.\n- We recommend using key:value pairs.\n- Provided pairs will be considered for inclusion as future slots/terms in this data\n collection template.\nexamples:\n- value: 'experimental treatment: value'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000008\n- MIXS:0000300\nrank: 7\nstring_serialization: '{text}'\nalias: experimental_factor_other\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nThe number of exterior doors in the built structure
URI: MIXS:0000170
"},{"location":"ext_door/#inheritance","title":"Inheritance","text":"name: ext_door\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of exterior doors in the built structure\ntitle: exterior door count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exterior door count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000170\nalias: ext_door\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe orientation of the exterior wall
URI: MIXS:0000817
"},{"location":"ext_wall_orient/#inheritance","title":"Inheritance","text":"name: ext_wall_orient\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The orientation of the exterior wall\ntitle: orientations of exterior wall\nexamples:\n- value: northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior wall\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000817\nalias: ext_wall_orient\ndomain_of:\n- Biosample\nrange: ext_wall_orient_enum\nmultivalued: false\n\nThe compass direction the exterior window of the room is facing
URI: MIXS:0000818
"},{"location":"ext_window_orient/#inheritance","title":"Inheritance","text":"name: ext_window_orient\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The compass direction the exterior window of the room is facing\ntitle: orientations of exterior window\nexamples:\n- value: southwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior window\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000818\nalias: ext_window_orient\ndomain_of:\n- Biosample\nrange: ext_window_orient_enum\nmultivalued: false\n\nLink to corresponding identifier in external database
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:external_database_identifiers
"},{"location":"external_database_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: external_database_identifiers\ndescription: Link to corresponding identifier in external database\nnotes:\n- had tried ranges of external identifier and string\ncomments:\n- The value of this field is always a registered CURIE\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- skos:closeMatch\nrank: 1000\nis_a: alternative_identifiers\nabstract: true\nalias: external_database_identifiers\ndomain_of:\n- ProcessedSample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nProvides the target biomolecule that has been separated from a sample during an extraction process.
URI: nmdc:extraction_targets
"},{"location":"extraction_targets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"extraction_targets/#properties","title":"Properties","text":"Range: ExtractionTargetEnum
Multivalued: True
name: extraction_targets\ndescription: Provides the target biomolecule that has been separated from a sample\n during an extraction process.\nnotes:\n- todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)\nfrom_schema: https://w3id.org/nmdc/nmdc\nnarrow_mappings:\n- NCIT:C177560\n- MIXS:0000037\nrank: 1000\nalias: extraction_targets\ndomain_of:\n- Extraction\nrange: ExtractionTargetEnum\nmultivalued: true\n\nUnusual physical events that may have affected microbial populations
URI: MIXS:0000320
"},{"location":"extreme_event/#inheritance","title":"Inheritance","text":"name: extreme_event\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Unusual physical events that may have affected microbial populations\ntitle: history/extreme events\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/extreme events\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000320\nalias: extreme_event\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nSoil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups
URI: MIXS:0001083
"},{"location":"fao_class/#inheritance","title":"Inheritance","text":"name: fao_class\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Soil classification from the FAO World Reference Database for Soil Resources.\n The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\ntitle: soil_taxonomic/FAO classification\nexamples:\n- value: Luvisols\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/FAO classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001083\nalias: fao_class\ndomain_of:\n- Biosample\nrange: fao_class_enum\nmultivalued: false\n\nA Sequence Ontology term that describes the category of a feature
URI: nmdc:feature_category
"},{"location":"feature_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no FunctionalAnnotation An assignment of a function term (e no"},{"location":"feature_category/#properties","title":"Properties","text":"name: feature_category\ndescription: A Sequence Ontology term that describes the category of a feature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_category\ndomain_of:\n- GenomeFeature\n- FunctionalAnnotation\nrange: ControlledIdentifiedTermValue\n\nTODO: Yuri to write
URI: nmdc:feature_type
"},{"location":"feature_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"feature_type/#properties","title":"Properties","text":"name: feature_type\ndescription: 'TODO: Yuri to write'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_type\ndomain_of:\n- GenomeFeature\nrange: string\n\nInformation about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens
URI: MIXS:0000556
"},{"location":"fertilizer_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: fertilizer_regm\nannotations:\n expected_value:\n tag: expected_value\n value: fertilizer name;fertilizer amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the use of fertilizers; should\n include the name of fertilizer, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple fertilizer regimens\ntitle: fertilizer regimen\nexamples:\n- value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fertilizer regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000556\nalias: fertilizer_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nName of the hydrocarbon field (e.g. Albacora)
URI: MIXS:0000291
"},{"location":"field/#inheritance","title":"Inheritance","text":"name: field\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the hydrocarbon field (e.g. Albacora)\ntitle: field name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- field name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000291\nalias: field\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:field_research_site_set
"},{"location":"field_research_site_set/#inheritance","title":"Inheritance","text":"Range: FieldResearchSite
Multivalued: True
name: field_research_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: field_research_site_set\ndomain_of:\n- Database\nrange: FieldResearchSite\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nSize of the file in bytes
URI: nmdc:file_size_bytes
"},{"location":"file_size_bytes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"file_size_bytes/#properties","title":"Properties","text":"name: file_size_bytes\ndescription: Size of the file in bytes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: file_size_bytes\ndomain_of:\n- DataObject\nrange: bytes\n\nA porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained.
URI: nmdc:filter_material
"},{"location":"filter_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filter_material/#properties","title":"Properties","text":"name: filter_material\ndescription: A porous material on which solid particles present in air or other fluid\n which flows through it are largely caught and retained.\ncomments:\n- 'Filters are made with a variety of materials: cellulose and derivatives, glass\n fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous or\n be made so by mechanical or other means. Membrane/ceramic filters are prepared with\n highly controlled pore size in a sheet of suitable material such as polyfluoroethylene,\n polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement.\n The pores constitute 80\u201385% of the filter volume commonly and several pore sizes\n are available for air sampling (0.45\u22120.8 \u03bcm are commonly employed).'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filter_material\ndomain_of:\n- FiltrationProcess\nrange: string\n\nType of filter used or how the sample was filtered
URI: nmdc:filter_method
"},{"location":"filter_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"filter_method/#properties","title":"Properties","text":"Range: String
Recommended: True
name: filter_method\ndescription: Type of filter used or how the sample was filtered\ntitle: filter method\ncomments:\n- describe the filter or provide a catalog number and manufacturer\nexamples:\n- value: C18\n- value: Basix PES, 13-100-106 FisherSci\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000765\nrank: 6\nstring_serialization: '{text}'\nalias: filter_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nA quantitative or qualitative measurement of the physical dimensions of the pores in a material.
URI: nmdc:filter_pore_size
"},{"location":"filter_pore_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filter_pore_size/#properties","title":"Properties","text":"name: filter_pore_size\ndescription: A quantitative or qualitative measurement of the physical dimensions\n of the pores in a material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filter_pore_size\ndomain_of:\n- FiltrationProcess\nrange: QuantityValue\n\nA device which removes solid particulates or airborne molecular contaminants
URI: MIXS:0000765
"},{"location":"filter_type/#inheritance","title":"Inheritance","text":"Range: FilterTypeEnum
Multivalued: True
name: filter_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: A device which removes solid particulates or airborne molecular contaminants\ntitle: filter type\nexamples:\n- value: HEPA\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- filter type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000765\nalias: filter_type\ndomain_of:\n- Biosample\nrange: filter_type_enum\nmultivalued: true\n\nThe type of conditioning applied to a filter, device, etc.
URI: nmdc:filtration_category
"},{"location":"filtration_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filtration_category/#properties","title":"Properties","text":"name: filtration_category\ndescription: The type of conditioning applied to a filter, device, etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filtration_category\ndomain_of:\n- FiltrationProcess\nrange: string\n\nWhen solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in the combination
URI: nmdc:final_concentration
"},{"location":"final_concentration/#inheritance","title":"Inheritance","text":"name: final_concentration\ndescription: When solutions A (containing substance X) and B are combined together,\n this slot captures the concentration of X in the combination\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: concentration\nalias: final_concentration\ndomain_of:\n- PortionOfSubstance\nrange: QuantityValue\n\nHistorical and/or physical evidence of fire
URI: MIXS:0001086
"},{"location":"fire/#inheritance","title":"Inheritance","text":"name: fire\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Historical and/or physical evidence of fire\ntitle: history/fire\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/fire\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001086\nalias: fire\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nA firebox with chimney
URI: MIXS:0000802
"},{"location":"fireplace_type/#inheritance","title":"Inheritance","text":"name: fireplace_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A firebox with chimney\ntitle: fireplace type\nexamples:\n- value: wood burning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fireplace type\nrank: 1000\nis_a: core field\nstring_serialization: '[gas burning|wood burning]'\nslot_uri: MIXS:0000802\nalias: fireplace_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nHistorical and/or physical evidence of flooding
URI: MIXS:0000319
"},{"location":"flooding/#inheritance","title":"Inheritance","text":"name: flooding\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Historical and/or physical evidence of flooding\ntitle: history/flooding\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/flooding\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000319\nalias: flooding\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe time period since installment of the carpet or flooring
URI: MIXS:0000164
"},{"location":"floor_age/#inheritance","title":"Inheritance","text":"name: floor_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: years, weeks, days\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The time period since installment of the carpet or flooring\ntitle: floor age\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000164\nalias: floor_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe area of the floor space within the room
URI: MIXS:0000165
"},{"location":"floor_area/#inheritance","title":"Inheritance","text":"name: floor_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The area of the floor space within the room\ntitle: floor area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000165\nalias: floor_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000803
"},{"location":"floor_cond/#inheritance","title":"Inheritance","text":"name: floor_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the floor at the time of sampling; photos or\n video preferred; use drawings to indicate location of damaged areas\ntitle: floor condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000803\nalias: floor_cond\ndomain_of:\n- Biosample\nrange: floor_cond_enum\nmultivalued: false\n\nThe number of floors in the building, including basements and mechanical penthouse
URI: MIXS:0000225
"},{"location":"floor_count/#inheritance","title":"Inheritance","text":"name: floor_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of floors in the building, including basements and mechanical\n penthouse\ntitle: floor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000225\nalias: floor_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe floor covering type; the finished surface that is walked on
URI: MIXS:0000804
"},{"location":"floor_finish_mat/#inheritance","title":"Inheritance","text":"name: floor_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The floor covering type; the finished surface that is walked on\ntitle: floor finish material\nexamples:\n- value: carpet\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000804\nalias: floor_finish_mat\ndomain_of:\n- Biosample\nrange: floor_finish_mat_enum\nmultivalued: false\n\nRefers to the structural elements and subfloor upon which the finish flooring is installed
URI: MIXS:0000806
"},{"location":"floor_struc/#inheritance","title":"Inheritance","text":"name: floor_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the structural elements and subfloor upon which the finish\n flooring is installed\ntitle: floor structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000806\nalias: floor_struc\ndomain_of:\n- Biosample\nrange: floor_struc_enum\nmultivalued: false\n\nThe ability of the floor to provide inertia against temperature fluctuations
URI: MIXS:0000166
"},{"location":"floor_thermal_mass/#inheritance","title":"Inheritance","text":"name: floor_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the floor to provide inertia against temperature fluctuations\ntitle: floor thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000166\nalias: floor_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSigns of the presence of mold or mildew in a room
URI: MIXS:0000805
"},{"location":"floor_water_mold/#inheritance","title":"Inheritance","text":"name: floor_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew in a room\ntitle: floor signs of water/mold\nexamples:\n- value: ceiling discoloration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor signs of water/mold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000805\nalias: floor_water_mold\ndomain_of:\n- Biosample\nrange: floor_water_mold_enum\nmultivalued: false\n\nRaw or converted fluorescence of water
URI: MIXS:0000704
"},{"location":"fluor/#inheritance","title":"Inheritance","text":"name: fluor\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram chlorophyll a per cubic meter, volts\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Raw or converted fluorescence of water\ntitle: fluorescence\nexamples:\n- value: 2.5 volts\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fluorescence\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000704\nalias: fluor\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.
URI: MIXS:0000226
"},{"location":"freq_clean/#inheritance","title":"Inheritance","text":"name: freq_clean\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration or {text}\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times the sample location is cleaned. Frequency of cleaning\n might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\ntitle: frequency of cleaning\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cleaning\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000226\nalias: freq_clean\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of times a meal is cooked per week
URI: MIXS:0000227
"},{"location":"freq_cook/#inheritance","title":"Inheritance","text":"name: freq_cook\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times a meal is cooked per week\ntitle: frequency of cooking\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cooking\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000227\nalias: freq_cook\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:functional_annotation_agg
"},{"location":"functional_annotation_agg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"functional_annotation_agg/#properties","title":"Properties","text":"Range: FunctionalAnnotationAggMember
Multivalued: True
name: functional_annotation_agg\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: functional_annotation_agg\ndomain_of:\n- Database\nrange: FunctionalAnnotationAggMember\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of all functional annotations
URI: nmdc:functional_annotation_set
"},{"location":"functional_annotation_set/#inheritance","title":"Inheritance","text":"Range: FunctionalAnnotation
Multivalued: True
name: functional_annotation_set\ndescription: This property links a database object to the set of all functional annotations\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: functional_annotation_set\ndomain_of:\n- Database\nrange: FunctionalAnnotation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants.
URI: nmdc:funding_sources
"},{"location":"funding_sources/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"funding_sources/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: funding_sources\ndescription: A list of organizations, along with the award numbers, that underwrite\n financial support for projects of a particular type. Typically, they process applications\n and award funds to the chosen qualified applicants.\ncomments:\n- Include only the name of the funding organization and the award or contract number.\nexamples:\n- value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n- value: U.S. Department of Energy, Office of Science, Office of Biological and Environmental\n Research (BER) under contract DE-AC05-00OR2275\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C39409\nrank: 1000\nalias: funding_sources\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\nInformation about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens
URI: MIXS:0000557
"},{"location":"fungicide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: fungicide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: fungicide name;fungicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of fungicides; should include\n the name of fungicide, amount administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple fungicide regimens\ntitle: fungicide regimen\nexamples:\n- value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fungicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000557\nalias: fungicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe types of furniture present in the sampled room
URI: MIXS:0000807
"},{"location":"furniture/#inheritance","title":"Inheritance","text":"name: furniture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The types of furniture present in the sampled room\ntitle: furniture\nexamples:\n- value: chair\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- furniture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000807\nalias: furniture\ndomain_of:\n- Biosample\nrange: furniture_enum\nmultivalued: false\n\nThe gap size percentage of all scaffolds.
URI: nmdc:gap_pct
"},{"location":"gap_pct/#inheritance","title":"Inheritance","text":"name: gap_pct\ndescription: The gap size percentage of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gap_pct\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nUse of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens
URI: MIXS:0000558
"},{"location":"gaseous_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gaseous_environment\nannotations:\n expected_value:\n tag: expected_value\n value: gaseous compound name;gaseous compound amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Use of conditions with differing gaseous environments; should include\n the name of gaseous compound, amount administered, treatment duration, interval\n and total experimental duration; can include multiple gaseous environment regimens\ntitle: gaseous environment\nexamples:\n- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000558\nalias: gaseous_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAmount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances
URI: MIXS:0000661
"},{"location":"gaseous_substances/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gaseous_substances\nannotations:\n expected_value:\n tag: expected_value\n value: gaseous substance name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount or concentration of substances such as hydrogen sulfide, carbon\n dioxide, methane, etc.; can include multiple substances\ntitle: gaseous substances\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous substances\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000661\nalias: gaseous_substances\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAverage of GC content of all contigs.
URI: nmdc:gc_avg
"},{"location":"gc_avg/#inheritance","title":"Inheritance","text":"name: gc_avg\ndescription: Average of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_avg\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nStandard deviation of GC content of all contigs.
URI: nmdc:gc_std
"},{"location":"gc_std/#inheritance","title":"Inheritance","text":"name: gc_std\ndescription: Standard deviation of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_std\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe gender type of the restroom
URI: MIXS:0000808
"},{"location":"gender_restroom/#inheritance","title":"Inheritance","text":"name: gender_restroom\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The gender type of the restroom\ntitle: gender of restroom\nexamples:\n- value: male\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gender of restroom\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000808\nalias: gender_restroom\ndomain_of:\n- Biosample\nrange: gender_restroom_enum\nmultivalued: false\n\nNumber of genes.
URI: nmdc:gene_count
"},{"location":"gene_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gene_count/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: gene_count\ndescription: Number of genes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_count\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nThe identifier for the gene function.
URI: nmdc:gene_function_id
"},{"location":"gene_function_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"gene_function_id/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
name: gene_function_id\ndescription: The identifier for the gene function.\nexamples:\n- value: KEGG.ORTHOLOGY:K00627\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_function_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: uriorcurie\nrequired: true\n\ncalibration information is generated a process
URI: nmdc:generates_calibration
"},{"location":"generates_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"generates_calibration/#properties","title":"Properties","text":"name: generates_calibration\ndescription: calibration information is generated a process\ncomments:\n- A gas chromatography mass spectromery run generates data to calibrate the retention\n index\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: generates_calibration\ndomain_of:\n- MassSpectrometry\nrange: CalibrationInformation\nstructured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n\nGenetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection
URI: MIXS:0000859
"},{"location":"genetic_mod/#inheritance","title":"Inheritance","text":"name: genetic_mod\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Genetic modifications of the genome of an organism, which may occur naturally\n by spontaneous mutation, or be introduced by some experimental means, e.g. specification\n of a transgene or the gene knocked-out or details of transient transfection\ntitle: genetic modification\nexamples:\n- value: aox1A transgenic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- genetic modification\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000859\nalias: genetic_mod\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThis property links a database object to the set of all features
URI: nmdc:genome_feature_set
"},{"location":"genome_feature_set/#inheritance","title":"Inheritance","text":"Range: GenomeFeature
Multivalued: True
name: genome_feature_set\ndescription: This property links a database object to the set of all features\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: genome_feature_set\ndomain_of:\n- Database\nrange: GenomeFeature\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)
URI: MIXS:0000010
"},{"location":"geo_loc_name/#inheritance","title":"Inheritance","text":"name: geo_loc_name\nannotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location name'\ndescription: The geographical origin of the sample as defined by the country or sea\n name followed by specific region name. Country or sea names should be chosen from\n the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)\ntitle: geographic location (country and/or sea,region)\nexamples:\n- value: 'USA: Maryland, Bethesda'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (country and/or sea,region)\nrank: 1000\nis_a: environment field\nstring_serialization: '{term}: {term}, {text}'\nslot_uri: MIXS:0000010\nalias: geo_loc_name\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA positive 1-based integer coordinate indicating start or end
URI: nmdc:gff_coordinate
"},{"location":"gff_coordinate/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: gff_coordinate\ndescription: A positive 1-based integer coordinate indicating start or end\ncomments:\n- For features that cross the origin of a circular feature (e.g. most bacterial genomes,\n plasmids, and some viral genomes), the requirement for start to be less than or\n equal to end is satisfied by making end = the position of the end + the length of\n the landmark feature.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gff_coordinate\nrange: integer\nminimum_value: 1\n\nThe url that points to the exact github location of a workflow.
URI: nmdc:git_url
"},{"location":"git_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NomAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAnnotation no MetaproteomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow yes"},{"location":"git_url/#properties","title":"Properties","text":"name: git_url\ndescription: The url that points to the exact github location of a workflow.\nexamples:\n- value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n- value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: git_url\ndomain_of:\n- WorkflowExecution\nrange: string\n\nMeasurement of glucosidase activity
URI: MIXS:0000137
"},{"location":"glucosidase_act/#inheritance","title":"Inheritance","text":"name: glucosidase_act\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mol per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of glucosidase activity\ntitle: glucosidase activity\nexamples:\n- value: 5 mol per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- glucosidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000137\nalias: glucosidase_act\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:gnps_identifiers
"},{"location":"gnps_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... None Study"},{"location":"gnps_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: gnps_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: gnps_identifiers\nrange: string\n\nidentifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results
URI: nmdc:gnps_task_identifiers
"},{"location":"gnps_task_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gnps\\.task:[a-f0-9]+$
name: gnps_task_identifiers\ndescription: identifiers that link a NMDC study to a web-based report about metabolomics\n analysis progress and results\ntitle: GNPS task identifiers\ncomments:\n- this could be considered a related identifier, as the metabolomics progress and\n results aren't a study per se\n- this identifier was registered with bioregistry but not identifiers.org\nexamples:\n- value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysis/\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gnps_identifiers\nalias: gnps_task_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^gnps\\.task:[a-f0-9]+$\n\nidentifiers for corresponding analysis projects in GOLD
URI: nmdc:gold_analysis_project_identifiers
"},{"location":"gold_analysis_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Ga[0-9]+$
name: gold_analysis_project_identifiers\ndescription: identifiers for corresponding analysis projects in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Ga0526289\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- gold_identifiers\nalias: gold_analysis_project_identifiers\ndomain_of:\n- MetagenomeAnnotation\n- MetatranscriptomeAnnotation\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Ga[0-9]+$\n\nidentifiers for corresponding sample in GOLD
URI: nmdc:gold_biosample_identifiers
"},{"location":"gold_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^gold:Gb[0-9]+$
name: gold_biosample_identifiers\ndescription: identifiers for corresponding sample in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gb0312930\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- gold_identifiers\nalias: gold_biosample_identifiers\ndomain_of:\n- Biosample\nrange: uriorcurie\nmultivalued: true\npattern: ^gold:Gb[0-9]+$\n\nURI: nmdc:gold_identifiers
"},{"location":"gold_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gold_study_identifiers identifiers for corresponding project(s) in GOLD None Study gold_biosample_identifiers identifiers for corresponding sample in GOLD uriorcurie Biosample gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD None NucleotideSequencing gold_analysis_project_identifiers identifiers for corresponding analysis projects in GOLD None MetagenomeAnnotation, MetatranscriptomeAnnotation"},{"location":"gold_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: gold_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: gold_identifiers\nrange: string\n\nThis is a grouping for any of the gold path fields
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:gold_path_field
"},{"location":"gold_path_field/#inheritance","title":"Inheritance","text":"name: gold_path_field\nannotations:\n tooltip:\n tag: tooltip\n value: GOLD Ecosystem Classification paths describe the surroundings from which\n an environmental sample or an organism is collected.\n annotations:\n source:\n tag: source\n value: https://gold.jgi.doe.gov/ecosystem_classification\ndescription: This is a grouping for any of the gold path fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: gold_path_field\nrange: string\n\nidentifiers for corresponding sequencing project in GOLD
URI: nmdc:gold_sequencing_project_identifiers
"},{"location":"gold_sequencing_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gp[0-9]+$
name: gold_sequencing_project_identifiers\ndescription: identifiers for corresponding sequencing project in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gp0108335\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: omics_processing_identifiers\nmixins:\n- gold_identifiers\nalias: gold_sequencing_project_identifiers\ndomain_of:\n- NucleotideSequencing\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Gp[0-9]+$\n\nidentifiers for corresponding project(s) in GOLD
URI: nmdc:gold_study_identifiers
"},{"location":"gold_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gs[0-9]+$
name: gold_study_identifiers\ndescription: identifiers for corresponding project(s) in GOLD\ntitle: GOLD Study Identifiers\ncomments:\n- uses the prefix GS (but possibly in a different case)\nexamples:\n- value: https://bioregistry.io/gold:Gs0110115\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/studies\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gold_identifiers\nalias: gold_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Gs[0-9]+$\n\nWhether or not subject is gravid, and if yes date due or date post-conception, specifying which is used
URI: MIXS:0000875
"},{"location":"gravidity/#inheritance","title":"Inheritance","text":"name: gravidity\nannotations:\n expected_value:\n tag: expected_value\n value: gravidity status;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Whether or not subject is gravid, and if yes date due or date post-conception,\n specifying which is used\ntitle: gravidity\nexamples:\n- value: yes;due date:2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravidity\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{timestamp}'\nslot_uri: MIXS:0000875\nalias: gravidity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments
URI: MIXS:0000559
"},{"location":"gravity/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gravity\nannotations:\n expected_value:\n tag: expected_value\n value: gravity factor value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter per square second, g\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of gravity factor to study\n various types of responses in presence, absence or modified levels of gravity; treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n treatments\ntitle: gravity\nexamples:\n- value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000559\nalias: gravity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nType of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research
URI: MIXS:0001043
"},{"location":"growth_facil/#inheritance","title":"Inheritance","text":"name: growth_facil\nannotations:\n expected_value:\n tag: expected_value\n value: free text or CO\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\ntitle: growth facility\nexamples:\n- value: Growth chamber [CO_715:0000189]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth facility\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{termLabel} {[termID]}'\nslot_uri: MIXS:0001043\nalias: growth_facil\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nCharacteristic shape, appearance or growth form of a plant species
URI: MIXS:0001044
"},{"location":"growth_habit/#inheritance","title":"Inheritance","text":"name: growth_habit\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Characteristic shape, appearance or growth form of a plant species\ntitle: growth habit\nexamples:\n- value: spreading\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth habit\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001044\nalias: growth_habit\ndomain_of:\n- Biosample\nrange: growth_habit_enum\nmultivalued: false\n\nInformation about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens
URI: MIXS:0000560
"},{"location":"growth_hormone_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: growth_hormone_regm\nannotations:\n expected_value:\n tag: expected_value\n value: growth hormone name;growth hormone amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of growth hormones; should\n include the name of growth hormone, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple growth hormone\n regimens\ntitle: growth hormone regimen\nexamples:\n- value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth hormone regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000560\nalias: growth_hormone_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTaxonomic class assigned by GTDB-Tk.
URI: nmdc:gtdbtk_class
"},{"location":"gtdbtk_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_class/#properties","title":"Properties","text":"name: gtdbtk_class\ndescription: Taxonomic class assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:class\nrank: 1000\nalias: gtdbtk_class\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic domain assigned by GTDB-Tk.
URI: nmdc:gtdbtk_domain
"},{"location":"gtdbtk_domain/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_domain/#properties","title":"Properties","text":"name: gtdbtk_domain\ndescription: Taxonomic domain assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:superkingdom\nrank: 1000\nalias: gtdbtk_domain\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic family assigned by GTDB-Tk.
URI: nmdc:gtdbtk_family
"},{"location":"gtdbtk_family/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_family/#properties","title":"Properties","text":"name: gtdbtk_family\ndescription: Taxonomic family assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:family\nrank: 1000\nalias: gtdbtk_family\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic genus assigned by GTDB-Tk.
URI: nmdc:gtdbtk_genus
"},{"location":"gtdbtk_genus/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_genus/#properties","title":"Properties","text":"name: gtdbtk_genus\ndescription: Taxonomic genus assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:genus\nrank: 1000\nalias: gtdbtk_genus\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic order assigned by GTDB-Tk.
URI: nmdc:gtdbtk_order
"},{"location":"gtdbtk_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_order/#properties","title":"Properties","text":"name: gtdbtk_order\ndescription: Taxonomic order assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:order\nrank: 1000\nalias: gtdbtk_order\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic phylum assigned by GTDB-Tk.
URI: nmdc:gtdbtk_phylum
"},{"location":"gtdbtk_phylum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_phylum/#properties","title":"Properties","text":"name: gtdbtk_phylum\ndescription: Taxonomic phylum assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:phylum\nrank: 1000\nalias: gtdbtk_phylum\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic genus assigned by GTDB-Tk.
URI: nmdc:gtdbtk_species
"},{"location":"gtdbtk_species/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_species/#properties","title":"Properties","text":"name: gtdbtk_species\ndescription: Taxonomic genus assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:species\nrank: 1000\nalias: gtdbtk_species\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:habitat
"},{"location":"habitat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment no"},{"location":"habitat/#properties","title":"Properties","text":"name: habitat\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: habitat\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: string\n\nThe total count of hallways and cooridors in the built structure
URI: MIXS:0000228
"},{"location":"hall_count/#inheritance","title":"Inheritance","text":"name: hall_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total count of hallways and cooridors in the built structure\ntitle: hallway/corridor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hallway/corridor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000228\nalias: hall_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe handidness of the individual sampled
URI: MIXS:0000809
"},{"location":"handidness/#inheritance","title":"Inheritance","text":"name: handidness\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The handidness of the individual sampled\ntitle: handidness\nexamples:\n- value: right handedness\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- handidness\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000809\nalias: handidness\ndomain_of:\n- Biosample\nrange: handidness_enum\nmultivalued: false\n\nLinks a quantity value to a boolean
URI: nmdc:has_boolean_value
"},{"location":"has_boolean_value/#properties","title":"Properties","text":"name: has_boolean_value\ndescription: Links a quantity value to a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_boolean_value\nrange: boolean\n\nThe identifier of the associated ChromatographyConfiguration, providing information about how a sample was introduced into the mass spectrometer.
URI: nmdc:has_chromatography_configuration
"},{"location":"has_chromatography_configuration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"has_chromatography_configuration/#properties","title":"Properties","text":"name: has_chromatography_configuration\ndescription: The identifier of the associated ChromatographyConfiguration, providing\n information about how a sample was introduced into the mass spectrometer.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_chromatography_configuration\ndomain_of:\n- MassSpectrometry\nrange: ChromatographyConfiguration\n\nThis slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study
URI: prov:qualifiedAssociation
"},{"location":"has_credit_associations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"has_credit_associations/#properties","title":"Properties","text":"Range: CreditAssociation
Multivalued: True
name: has_credit_associations\nannotations:\n tooltip:\n tag: tooltip\n value: Other researchers associated with this study.\ndescription: 'This slot links a study to a credit association. The credit association\n will be linked to a person value and to a CRediT Contributor Roles term. Overall\n semantics: person should get credit X for their participation in the study'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: prov:qualifiedAssociation\nalias: has_credit_associations\ndomain_of:\n- Study\nrange: CreditAssociation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:has_failure_categorization
"},{"location":"has_failure_categorization/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAnnotation no NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no LibraryPreparation no StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ProtocolExecution A PlannedProces that has PlannedProcess parts no MetaproteomicsAnalysis no PlannedProcess no"},{"location":"has_failure_categorization/#properties","title":"Properties","text":"Range: FailureCategorization
Multivalued: True
name: has_failure_categorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_failure_categorization\ndomain_of:\n- PlannedProcess\nrange: FailureCategorization\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:has_function
"},{"location":"has_function/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e yes"},{"location":"has_function/#properties","title":"Properties","text":"Range: String
Regex pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$
name: has_function\nnotes:\n- the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm,\n- but is actually taking string arguments in MongoDB,\n- and those are frequently fulltext, not CURIEs. MAM 2021-06-23\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_function\ndomain_of:\n- FunctionalAnnotation\nrange: string\npattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n\nAn input to a process.
URI: nmdc:has_input
"},{"location":"has_input/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... yes MetagenomeSequencing Initial sequencing activity that precedes any analysis yes FiltrationProcess The process of segregation of phases; e yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAnnotation yes NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no CollectingBiosamplesFromSite yes Pooling physical combination of several instances of like material yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no LibraryPreparation yes StorageProcess A planned process with the objective to preserve and protect material entitie... yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no WorkflowExecution Represents an instance of an execution of a particular workflow yes Extraction A material separation in which a desired component of an input material is se... yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ProtocolExecution A PlannedProces that has PlannedProcess parts yes MetaproteomicsAnalysis no PlannedProcess no"},{"location":"has_input/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: has_input\ndescription: An input to a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- input\nrank: 1000\nalias: has_input\ndomain_of:\n- PlannedProcess\nrange: NamedThing\nmultivalued: true\n\nThe identifier of the associated MassSpectrometryConfiguration.
URI: nmdc:has_mass_spectrometry_configuration
"},{"location":"has_mass_spectrometry_configuration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"has_mass_spectrometry_configuration/#properties","title":"Properties","text":"name: has_mass_spectrometry_configuration\ndescription: The identifier of the associated MassSpectrometryConfiguration.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_mass_spectrometry_configuration\ndomain_of:\n- MassSpectrometry\nrange: MassSpectrometryConfiguration\n\nThe maximum value part, expressed as number, of the quantity value when the value covers a range.
URI: nmdc:has_maximum_numeric_value
"},{"location":"has_maximum_numeric_value/#inheritance","title":"Inheritance","text":"name: has_maximum_numeric_value\ndescription: The maximum value part, expressed as number, of the quantity value when\n the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_maximum_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\nURI: nmdc:has_metabolite_identifications
"},{"location":"has_metabolite_identifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysis no"},{"location":"has_metabolite_identifications/#properties","title":"Properties","text":"Range: MetaboliteIdentification
Multivalued: True
name: has_metabolite_identifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_metabolite_identifications\ndomain_of:\n- MetabolomicsAnalysis\nrange: MetaboliteIdentification\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe minimum value part, expressed as number, of the quantity value when the value covers a range.
URI: nmdc:has_minimum_numeric_value
"},{"location":"has_minimum_numeric_value/#inheritance","title":"Inheritance","text":"name: has_minimum_numeric_value\ndescription: The minimum value part, expressed as number, of the quantity value when\n the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_minimum_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\nLinks a quantity value to a number
URI: nmdc:has_numeric_value
"},{"location":"has_numeric_value/#inheritance","title":"Inheritance","text":"name: has_numeric_value\ndescription: Links a quantity value to a number\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- qud:quantityValue\n- schema:value\nrank: 1000\nalias: has_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\nAn output from a process.
URI: nmdc:has_output
"},{"location":"has_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... yes MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAnnotation yes NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no CollectingBiosamplesFromSite yes Pooling physical combination of several instances of like material yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no LibraryPreparation yes StorageProcess A planned process with the objective to preserve and protect material entitie... yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no WorkflowExecution Represents an instance of an execution of a particular workflow yes Extraction A material separation in which a desired component of an input material is se... yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ProtocolExecution A PlannedProces that has PlannedProcess parts yes MetaproteomicsAnalysis no PlannedProcess no"},{"location":"has_output/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: has_output\ndescription: An output from a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- output\nrank: 1000\nalias: has_output\ndomain_of:\n- PlannedProcess\nrange: NamedThing\nmultivalued: true\n\nURI: nmdc:has_peptide_quantifications
","text":""},{"location":"has_peptide_quantifications/#properties","title":"Properties","text":"Range: PeptideQuantification
Multivalued: True
name: has_peptide_quantifications\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_peptide_quantifications\nrange: PeptideQuantification\nmultivalued: true\ninlined_as_list: true\n\nA list of process parts that make up a protocol.
URI: nmdc:has_process_parts
"},{"location":"has_process_parts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProtocolExecution A PlannedProces that has PlannedProcess parts yes"},{"location":"has_process_parts/#properties","title":"Properties","text":"Range: PlannedProcess
Multivalued: True
Required: True
name: has_process_parts\ndescription: A list of process parts that make up a protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: has_process_parts\ndomain_of:\n- ProtocolExecution\nrange: PlannedProcess\nrequired: true\nmultivalued: true\n\nThe value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"
URI: nmdc:has_raw_value
"},{"location":"has_raw_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ImageValue An attribute value representing an image no PersonValue An attribute value representing a person yes QuantityValue A simple quantity, e yes TextValue A basic string value no GeolocationValue A normalized value for a location on the earth's surface yes ControlledTermValue A controlled term or class from an ontology no TimestampValue A value that is a timestamp no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no AttributeValue The value for any value of a attribute for a sample no"},{"location":"has_raw_value/#properties","title":"Properties","text":"name: has_raw_value\ndescription: The value that was specified for an annotation in raw form, i.e. a string.\n E.g. \"2 cm\" or \"2-4 cm\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_raw_value\ndomain_of:\n- AttributeValue\nrange: string\n\nLinks a QuantityValue to a unit
URI: nmdc:has_unit
"},{"location":"has_unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e yes"},{"location":"has_unit/#properties","title":"Properties","text":"name: has_unit\ndescription: Links a QuantityValue to a unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- scale\nmappings:\n- qud:unit\n- schema:unitCode\nrank: 1000\nalias: has_unit\ndomain_of:\n- QuantityValue\nrange: unit\n\nMain hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000989
"},{"location":"hc_produced/#inheritance","title":"Inheritance","text":"name: hc_produced\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n etc). If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: hydrocarbon type produced\nexamples:\n- value: Gas\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon type produced\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000989\nalias: hc_produced\ndomain_of:\n- Biosample\nrange: hc_produced_enum\nmultivalued: false\n\nMain Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000988
"},{"location":"hcr/#inheritance","title":"Inheritance","text":"name: hcr\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined\n as a natural environmental feature containing large amounts of hydrocarbons at high\n concentrations potentially suitable for commercial exploitation. This term should\n not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich\n environments with currently limited commercial interest such as seeps, outcrops,\n gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\"\n field\ntitle: hydrocarbon resource type\nexamples:\n- value: Oil Sand\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000988\nalias: hcr\ndomain_of:\n- Biosample\nrange: hcr_enum\nmultivalued: false\n\nOriginal formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS
URI: MIXS:0000406
"},{"location":"hcr_fw_salinity/#inheritance","title":"Inheritance","text":"name: hcr_fw_salinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original formation water salinity (prior to secondary recovery e.g. Waterflooding)\n expressed as TDS\ntitle: formation water salinity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- formation water salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000406\nalias: hcr_fw_salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nGeological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000993
"},{"location":"hcr_geol_age/#inheritance","title":"Inheritance","text":"name: hcr_geol_age\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: hydrocarbon resource geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000993\nalias: hcr_geol_age\ndomain_of:\n- Biosample\nrange: hcr_geol_age_enum\nmultivalued: false\n\nOriginal pressure of the hydrocarbon resource
URI: MIXS:0000395
"},{"location":"hcr_pressure/#inheritance","title":"Inheritance","text":"name: hcr_pressure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: atmosphere, kilopascal\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original pressure of the hydrocarbon resource\ntitle: hydrocarbon resource original pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original pressure\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000395\nalias: hcr_pressure\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nOriginal temperature of the hydrocarbon resource
URI: MIXS:0000393
"},{"location":"hcr_temp/#inheritance","title":"Inheritance","text":"name: hcr_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original temperature of the hydrocarbon resource\ntitle: hydrocarbon resource original temperature\nexamples:\n- value: 150-295 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original temperature\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000393\nalias: hcr_temp\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMethods of conditioning or heating a room or building
URI: MIXS:0000766
"},{"location":"heat_cool_type/#inheritance","title":"Inheritance","text":"Range: HeatCoolTypeEnum
Multivalued: True
name: heat_cool_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Methods of conditioning or heating a room or building\ntitle: heating and cooling system type\nexamples:\n- value: heat pump\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating and cooling system type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000766\nalias: heat_cool_type\ndomain_of:\n- Biosample\nrange: heat_cool_type_enum\nmultivalued: true\n\nThe location of heat delivery within the room
URI: MIXS:0000810
"},{"location":"heat_deliv_loc/#inheritance","title":"Inheritance","text":"name: heat_deliv_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The location of heat delivery within the room\ntitle: heating delivery locations\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating delivery locations\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000810\nalias: heat_deliv_loc\ndomain_of:\n- Biosample\nrange: heat_deliv_loc_enum\nmultivalued: false\n\nThe method by which the heat is delivered through the system
URI: MIXS:0000812
"},{"location":"heat_sys_deliv_meth/#inheritance","title":"Inheritance","text":"name: heat_sys_deliv_meth\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The method by which the heat is delivered through the system\ntitle: heating system delivery method\nexamples:\n- value: radiant\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system delivery method\nrank: 1000\nis_a: core field\nstring_serialization: '[conductive|radiant]'\nslot_uri: MIXS:0000812\nalias: heat_sys_deliv_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe heating system identifier
URI: MIXS:0000833
"},{"location":"heat_system_id/#inheritance","title":"Inheritance","text":"name: heat_system_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The heating system identifier\ntitle: heating system identifier\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000833\nalias: heat_system_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nHeavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.
URI: MIXS:0000652
"},{"location":"heavy_metals/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: heavy_metals\nannotations:\n expected_value:\n tag: expected_value\n value: heavy metal name;measurement value unit\n preferred_unit:\n tag: preferred_unit\n value: microgram per gram\n occurrence:\n tag: occurrence\n value: m\ndescription: Heavy metals present in the sequenced sample and their concentrations.\n For multiple heavy metals and concentrations, add multiple copies of this field.\ntitle: extreme_unusual_properties/heavy metals\nexamples:\n- value: mercury;0.09 micrograms per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000652\nalias: heavy_metals\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nReference or method used in determining heavy metals
URI: MIXS:0000343
"},{"location":"heavy_metals_meth/#inheritance","title":"Inheritance","text":"name: heavy_metals_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining heavy metals\ntitle: extreme_unusual_properties/heavy metals method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000343\nalias: heavy_metals_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\ninlined: true\ninlined_as_list: true\n\nThe average carpet fiber height in the indoor environment
URI: MIXS:0000167
"},{"location":"height_carper_fiber/#inheritance","title":"Inheritance","text":"name: height_carper_fiber\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average carpet fiber height in the indoor environment\ntitle: height carpet fiber mat\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- height carpet fiber mat\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000167\nalias: height_carper_fiber\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000561
"},{"location":"herbicide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: herbicide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: herbicide name;herbicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of herbicides; information\n about treatment involving use of growth hormones; should include the name of herbicide,\n amount administered, treatment regimen including how many times the treatment was\n repeated, how long each treatment lasted, and the start and end time of the entire\n treatment; can include multiple regimens\ntitle: herbicide regimen\nexamples:\n- value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- herbicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000561\nalias: herbicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:highest_similarity_score
"},{"location":"highest_similarity_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"highest_similarity_score/#properties","title":"Properties","text":"name: highest_similarity_score\ntodos:\n- Yuri to fill in description\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: highest_similarity_score\ndomain_of:\n- MetaboliteIdentification\nrange: float\n\nThe website address (URL) of an entity's homepage.
URI: nmdc:homepage_website
"},{"location":"homepage_website/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
Regex pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$
name: homepage_website\ndescription: The website address (URL) of an entity's homepage.\nexamples:\n- value: https://www.neonscience.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: websites\nalias: homepage_website\ndomain_of:\n- Study\nrange: string\nmultivalued: true\npattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\nmaximum_cardinality: 1\n\nReference or method used in determining the horizon
URI: MIXS:0000321
"},{"location":"horizon_meth/#inheritance","title":"Inheritance","text":"name: horizon_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the horizon\ntitle: soil horizon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000321\nalias: horizon_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nAge of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees
URI: MIXS:0000255
"},{"location":"host_age/#inheritance","title":"Inheritance","text":"name: host_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year, day, hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Age of host at the time of sampling; relevant scale depends on species\n and study, e.g. Could be seconds for amoebae or centuries for trees\ntitle: host age\nexamples:\n- value: 10 days\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000255\nalias: host_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nOriginal body habitat where the sample was obtained from
URI: MIXS:0000866
"},{"location":"host_body_habitat/#inheritance","title":"Inheritance","text":"name: host_body_habitat\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original body habitat where the sample was obtained from\ntitle: host body habitat\nexamples:\n- value: nasopharynx\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body habitat\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000866\nalias: host_body_habitat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSubstance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon
URI: MIXS:0000888
"},{"location":"host_body_product/#inheritance","title":"Inheritance","text":"name: host_body_product\nannotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Substance produced by the body, e.g. Stool, mucus, where the sample was\n obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or\n https://www.ebi.ac.uk/ols/ontologies/uberon\ntitle: host body product\nexamples:\n- value: mucus [UBERON:0000912]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body product\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000888\nalias: host_body_product\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nName of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
URI: MIXS:0000867
"},{"location":"host_body_site/#inheritance","title":"Inheritance","text":"name: host_body_site\nannotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of body site where the sample was obtained from, such as a specific\n organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\ntitle: host body site\nexamples:\n- value: gill [UBERON:0002535]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body site\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000867\nalias: host_body_site\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nCore body temperature of the host when sample was collected
URI: MIXS:0000274
"},{"location":"host_body_temp/#inheritance","title":"Inheritance","text":"name: host_body_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Core body temperature of the host when sample was collected\ntitle: host body temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000274\nalias: host_body_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe color of host
URI: MIXS:0000260
"},{"location":"host_color/#inheritance","title":"Inheritance","text":"name: host_color\nannotations:\n expected_value:\n tag: expected_value\n value: color\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The color of host\ntitle: host color\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host color\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000260\nalias: host_color\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nCommon name of the host.
URI: MIXS:0000248
"},{"location":"host_common_name/#inheritance","title":"Inheritance","text":"name: host_common_name\nannotations:\n expected_value:\n tag: expected_value\n value: common name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Common name of the host.\ntitle: host common name\nexamples:\n- value: human\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host common name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000248\nalias: host_common_name\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nType of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
URI: MIXS:0000869
"},{"location":"host_diet/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: host_diet\nannotations:\n expected_value:\n tag: expected_value\n value: diet type\n occurrence:\n tag: occurrence\n value: m\ndescription: Type of diet depending on the host, for animals omnivore, herbivore etc.,\n for humans high-fat, meditteranean etc.; can include multiple diet types\ntitle: host diet\nexamples:\n- value: herbivore\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host diet\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000869\nalias: host_diet\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nList of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text
URI: MIXS:0000031
"},{"location":"host_disease_stat/#inheritance","title":"Inheritance","text":"name: host_disease_stat\nannotations:\n expected_value:\n tag: expected_value\n value: disease name or Disease Ontology term\ndescription: List of diseases with which the host has been diagnosed; can include\n multiple diagnoses. The value of the field depends on host; for humans the terms\n should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,\n non-human host diseases are free text\ntitle: host disease status\nexamples:\n- value: rabies [DOID:11260]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host disease status\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000031\nalias: host_disease_stat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMeasurement of dry mass
URI: MIXS:0000257
"},{"location":"host_dry_mass/#inheritance","title":"Inheritance","text":"name: host_dry_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of dry mass\ntitle: host dry mass\nexamples:\n- value: 500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host dry mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000257\nalias: host_dry_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nFamilial relationships to other hosts in the same study; can include multiple relationships
URI: MIXS:0000872
"},{"location":"host_family_relation/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_family_relation\nannotations:\n expected_value:\n tag: expected_value\n value: relationship type;arbitrary identifier\n occurrence:\n tag: occurrence\n value: m\ndescription: Familial relationships to other hosts in the same study; can include\n multiple relationships\ntitle: host family relationship\nexamples:\n- value: offspring;Mussel25\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host family relationship\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0000872\nalias: host_family_relation\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\nObserved genotype
URI: MIXS:0000365
"},{"location":"host_genotype/#inheritance","title":"Inheritance","text":"name: host_genotype\nannotations:\n expected_value:\n tag: expected_value\n value: genotype\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Observed genotype\ntitle: host genotype\nexamples:\n- value: C57BL/6\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host genotype\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000365\nalias: host_genotype\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nLiterature reference giving growth conditions of the host
URI: MIXS:0000871
"},{"location":"host_growth_cond/#inheritance","title":"Inheritance","text":"name: host_growth_cond\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Literature reference giving growth conditions of the host\ntitle: host growth conditions\nexamples:\n- value: https://academic.oup.com/icesjms/article/68/2/349/617247\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host growth conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000871\nalias: host_growth_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe height of subject
URI: MIXS:0000264
"},{"location":"host_height/#inheritance","title":"Inheritance","text":"name: host_height\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The height of subject\ntitle: host height\nexamples:\n- value: 0.1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000264\nalias: host_height\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nContent of last meal and time since feeding; can include multiple values
URI: MIXS:0000870
"},{"location":"host_last_meal/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: host_last_meal\nannotations:\n expected_value:\n tag: expected_value\n value: content;duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Content of last meal and time since feeding; can include multiple values\ntitle: host last meal\nexamples:\n- value: corn feed;P2H\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host last meal\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000870\nalias: host_last_meal\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe length of subject
URI: MIXS:0000256
"},{"location":"host_length/#inheritance","title":"Inheritance","text":"name: host_length\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The length of subject\ntitle: host length\nexamples:\n- value: 1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host length\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000256\nalias: host_length\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDescription of life stage of host
URI: MIXS:0000251
"},{"location":"host_life_stage/#inheritance","title":"Inheritance","text":"name: host_life_stage\nannotations:\n expected_value:\n tag: expected_value\n value: stage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of life stage of host\ntitle: host life stage\nexamples:\n- value: adult\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host life stage\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000251\nalias: host_life_stage\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:host_name
"},{"location":"host_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_name/#properties","title":"Properties","text":"name: host_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: host_name\ndomain_of:\n- Biosample\nrange: string\n\nPhenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
URI: MIXS:0000874
"},{"location":"host_phenotype/#inheritance","title":"Inheritance","text":"name: host_phenotype\nannotations:\n expected_value:\n tag: expected_value\n value: PATO or HP\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Phenotype of human or other host. For phenotypic quality ontology (pato)\n (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For\n Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\ntitle: host phenotype\nexamples:\n- value: elongated [PATO:0001154]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host phenotype\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000874\nalias: host_phenotype\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nGender or physical sex of the host.
URI: MIXS:0000811
"},{"location":"host_sex/#inheritance","title":"Inheritance","text":"name: host_sex\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Gender or physical sex of the host.\ntitle: host sex\nexamples:\n- value: non-binary\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000811\nalias: host_sex\ndomain_of:\n- Biosample\nrange: host_sex_enum\nmultivalued: false\n\nMorphological shape of host
URI: MIXS:0000261
"},{"location":"host_shape/#inheritance","title":"Inheritance","text":"name: host_shape\nannotations:\n expected_value:\n tag: expected_value\n value: shape\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Morphological shape of host\ntitle: host shape\nexamples:\n- value: round\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host shape\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000261\nalias: host_shape\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA unique identifier by which each subject can be referred to, de-identified.
URI: MIXS:0000861
"},{"location":"host_subject_id/#inheritance","title":"Inheritance","text":"name: host_subject_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A unique identifier by which each subject can be referred to, de-identified.\ntitle: host subject id\nexamples:\n- value: MPI123\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subject id\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000861\nalias: host_subject_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.
URI: MIXS:0001318
"},{"location":"host_subspecf_genlin/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_subspecf_genlin\nannotations:\n expected_value:\n tag: expected_value\n value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n e.g. serovar, biotype, ecotype, variety, cultivar.\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about the genetic distinctness of the host organism below\n the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n or any relevant genetic typing schemes like Group I plasmid. Subspecies should not\n be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name\n and the lineage rank separated by a colon, e.g., biovar:abc123.\ntitle: host subspecific genetic lineage\nexamples:\n- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subspecific genetic lineage\nrank: 1000\nis_a: core field\nstring_serialization: '{rank name}:{text}'\nslot_uri: MIXS:0001318\nalias: host_subspecf_genlin\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\nThe growth substrate of the host.
URI: MIXS:0000252
"},{"location":"host_substrate/#inheritance","title":"Inheritance","text":"name: host_substrate\nannotations:\n expected_value:\n tag: expected_value\n value: substrate name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The growth substrate of the host.\ntitle: host substrate\nexamples:\n- value: rock\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host substrate\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000252\nalias: host_substrate\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.
URI: MIXS:0001298
"},{"location":"host_symbiont/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_symbiont\nannotations:\n expected_value:\n tag: expected_value\n value: species name or common name\n occurrence:\n tag: occurrence\n value: m\ndescription: The taxonomic name of the organism(s) found living in mutualistic, commensalistic,\n or parasitic symbiosis with the specific host.\ntitle: observed host symbionts\nexamples:\n- value: flukeworms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed host symbionts\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001298\nalias: host_symbiont\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\nNCBI taxon id of the host, e.g. 9606
URI: MIXS:0000250
"},{"location":"host_taxid/#inheritance","title":"Inheritance","text":"name: host_taxid\nannotations:\n expected_value:\n tag: expected_value\n value: NCBI taxon identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: NCBI taxon id of the host, e.g. 9606\ntitle: host taxid\ncomments:\n- Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host taxid\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000250\nalias: host_taxid\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nTotal mass of the host at collection, the unit depends on host
URI: MIXS:0000263
"},{"location":"host_tot_mass/#inheritance","title":"Inheritance","text":"name: host_tot_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total mass of the host at collection, the unit depends on host\ntitle: host total mass\nexamples:\n- value: 2500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host total mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000263\nalias: host_tot_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of wet mass
URI: MIXS:0000567
"},{"location":"host_wet_mass/#inheritance","title":"Inheritance","text":"name: host_wet_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of wet mass\ntitle: host wet mass\nexamples:\n- value: 1500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host wet mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000567\nalias: host_wet_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nAmount of water vapour in the air, at the time of sampling
URI: MIXS:0000100
"},{"location":"humidity/#inheritance","title":"Inheritance","text":"name: humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Amount of water vapour in the air, at the time of sampling\ntitle: humidity\nexamples:\n- value: 25 gram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000100\nalias: humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000568
"},{"location":"humidity_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: humidity_regm\nannotations:\n expected_value:\n tag: expected_value\n value: humidity value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to varying degree of\n humidity; information about treatment involving use of growth hormones; should include\n amount of humidity administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end time\n of the entire treatment; can include multiple regimens\ntitle: humidity regimen\nexamples:\n- value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000568\nalias: humidity_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
URI: nmdc:id
"},{"location":"id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Manifest A qualified collection of DataObjects that can be analyzed together in the sa... yes OrthologyGroup A set of genes or gene products in which all members are orthologous no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis yes FiltrationProcess The process of segregation of phases; e yes MaterialEntity no ProcessedSample yes NamedThing a databased entity or concept/class no Configuration A set of parameters that define the actions of a process and is shared among ... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no GeneProduct A molecule encoded by a gene that has an evolved function no MetatranscriptomeAnnotation yes EnvironmentalMaterialTerm no NomAnalysis yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... yes Study A study summarizes the overall goal of a research initiative and outlines the... yes CollectingBiosamplesFromSite yes Pooling physical combination of several instances of like material yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes ChemicalEntity An atom or molecule that can be represented with a chemical formula no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated yes OntologyClass A representation of class defined in an external ontology yes MetabolomicsAnalysis yes ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... yes ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... yes CalibrationInformation A calibration object that is associated with a process yes LibraryPreparation yes MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes StorageProcess A planned process with the objective to preserve and protect material entitie... yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no MetatranscriptomeAssembly yes Biosample Biological source material which can be characterized by an experiment yes WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... yes FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no DataObject An object that primarily consists of symbols that represent information yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component yes Instrument A material entity that is designed to perform a function in a scientific inve... yes ProtocolExecution A PlannedProces that has PlannedProcess parts yes Sample A sample is a material entity that can be characterized by an experiment no Site no MetaproteomicsAnalysis yes PlannedProcess no"},{"location":"id/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: id\ndescription: A unique identifier for a thing. Must be either a CURIE shorthand for\n a URI or a complete URI\nnotes:\n- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n- minting authority shoulders should probably be enumerated and checked in the pattern\nexamples:\n- value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\nfrom_schema: https://w3id.org/nmdc/nmdc\nstructured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- NamedThing\nrange: uriorcurie\nrequired: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nIdentifiers are crucial for the NMDC, both for any data objects created (aka minted) and for any external objects that are being referenced in NMDC.
Examples of entities that require identifiers:
Identifiers should be:
See McMurry et al, PMID:28662064 for more desiderata.
"},{"location":"identifiers/#curies-prefixed-ids","title":"CURIEs - prefixed IDs","text":"Following McMurry et al. we adopt the use of prefixed identifiers
The syntax is:
Prefix:LocalId\nExamples:
These prefixed identifiers are also known as CURIEs (Compact URIs). There is a W3C specification for these.
All prefixes should be registered with at least one standard identifier prefix system. If a prefix is not already registered, please open a ticket at Bioregistry.io to request registration. If an entity is registered in multiple registries (possibly with differing syntax or case), we recommend using the bioregistry.io registry as the primary source of truth.
Popular choices for identifier registry services include:
BIOSAMPLE:SAMEA2397676)","text":"Description Registry Entry Resolvable Link Bioregistry.io https://bioregistry.io/registry/biosample https://bioregistry.io/biosample:SAMEA2397676 Identifiers.org https://registry.identifiers.org/registry/biosample https://identifiers.org/BIOSAMPLE:SAMEA2397676 N2T.net http://n2t.net/BIOSAMPLE:SAMEA2397676"},{"location":"identifiers/#2-gold-identifiers-example-curie-goldgp0119849","title":"2. GOLD identifiers (Example CURIE: GOLD:Gp0119849)","text":"Description Registry Entry Resolvable Link Bioregistry.io https://bioregistry.io/registry/gold https://bioregistry.io/gold:Gp0119849 Identifiers.org https://registry.identifiers.org/registry/gold https://identifiers.org/GOLD:Gp0119849 N2T.net N/A http://n2t.net/GOLD:Gp0119849"},{"location":"identifiers/#identifiers-for-ontology-terms-and-function-descriptors","title":"identifiers for ontology terms and function descriptors","text":"Most of the ontologies we use are in OBO. All OBO IDs are prefixed using the ontology ID space. The list of ID spaces can be found on: http://obofoundry.org, and use a special resolver service called \"PURL\" (Permanent URL) to resolve the ID to a URL.
For example the ID/CURIE ENVO:00002007 represents the class sediment and is expanded to a URI of http://purl.obolibrary.org/obo/ENVO_00002007
KEGG is actually a set of databases, each with its own prefix, usually of form KEGG.$database, e.g.
The NMDC Schema is annotated with the set of IDs, ordered by preference, that are allowed to act as primary keys for instances of each class. For example the class OrthologyGroup has a description of the IDs allowed on the class web page, the first listed is KEGG.ORTHOLOGY. The full URL for each is in the jsonld context file, jsonschema/nmdc.context.jsonld.
The underlying yaml looks like this:
orthology group:\n is_a: functional annotation term\n description: >-\n A set of genes or gene products in which all members are orthologous\n id_prefixes:\n - KEGG.ORTHOLOGY ## KO number\n - EGGNOG\n - PFAM\n - TIGRFAM\n - SUPFAM\n - PANTHER.FAMILY\n exact_mappings:\n - biolink:GeneFamily\nThe NMDC Schema specifies legal identifiers for all of its classes. All data instances/records that are intended for upload into the NMDC metadata store must have an id field that follows this specification. Ids that are minted at NMDC must match this abstract pattern:
nmdc:<type-code>-<shoulder>-<blade><.version><_locus>\nThe abstract pattern has six parts, delimited by hyphens (unless otherwise specified):
nmdc: All NMDC identifiers will begin with this static prefix.
<typecode>: An alphabetical code with a 1:1 correspondence to a class from the NMDC Schema. Answers the question \"of what class is the data record that bears this id\"? Must consist of 1 to 6 lower case letters, although a minimum of 3 letters is suggested. The type code portion of an NMDC id must match the regular expression [a-z]{1,6}.
<shoulder>: A code that indicates what organization minted the identifier. Shoulder values must be zero to six lower case letters, flanked by one digit on either side. Answers the question \"what organization minted this id\"? The central identifier endpoint, hosted at LBL, uses the shoulder 00. Should organizations like JGI or EMSL need to mint identifiers in bulk, they would be assigned other shoulders, so that id values aren't reused. The shoulder portion of an NMDC id must match the regular expression [0-9][a-z]{0,6}[0-9].
<blade>: The fully unique part of the identifier under a given type code and shoulder namespace. The shoulder and blade together make up the key of the identifier. The blade is an alphanumeric string of open-ended length with at least one character, following the regular expression: [A-Za-z0-9]+.
<.version>: Differentiates multiple iterations of a workflow. The delimiter used to separate the version from the blade and everything before it is a dot (.). The version is a potentially repeating alphanumeric pattern with a minimum length of 1 character. The version portion of an NMDC id must match the regular expression (\\.[A-Za-z0-9]+)*.
<_locus>: Indicates the contig on which a genomic feature is found, along with its start and end coordinates. Delimited from the rest of the id by an underscore (_). The locus part, if present, must have at least one character from the set off uppercase letters, lower case letters, digits, underscores (_), dots (.) and hyphens (-). The regular expression that the locus will follow is: _[A-Za-z0-9_\\.-]+.
The per-part regular expression described above can be composed into one complete regular expression. Named capture groups have been used to tie in the part names.
^(?<prefix>nmdc):(?<typecode>[a-z]{1,6})-(?<shoulder>[0-9][a-z]{0,6}[0-9])-(?<blade>[A-Za-z0-9]+)(?<version>(\\.[A-Za-z0-9]+)*)(?<locus>_[A-Za-z0-9_\\.-]+)?$\nNMDC offers a central identifier minting endpoint in order to save data contributors the trouble of hand-crafting ids. The possibility of decentralized (or offline) minting of ids by trusted organizations has also been anticipated. id component 3 below (the shoulder) is used to indicate the organization that minted an id. LBL, which hosts the id minting endpoint will use one shoulder value. If another organization, like JGI or EMSL, needs to bulk-create ids outside of the central identifier minting endpoint, they would use different shoulders, to be determined by the NMDC Schema and metadata team.
Both metaG and metaT analyses produce GFF3 files. See issue 184 for more on how the GFF is modeled.
The main entity identifier used in NMDC is the gene product ID. This identifier is used in functioanl annotations. This is typically a protein encoded by a CDS, e.g.
Ga0185794_41 GeneMark.hmm-2 v1.05 CDS 48 1037 56.13 + 0 ID=Ga0185794_41_48_1037;translation_table=11;start_type=ATG;product=5-methylthioadenosine/S-adenosylhomocysteine deaminase;product_source=KO:K12960;cath_funfam=3.20.20.140;cog=COG0402;ko=KO:K12960;ec_number=EC:3.5.4.28,EC:3.5.4.31;pfam=PF01979;superfamily=51338,51556\nNote: when processing GFF column 9 values, NMDC first ensures that each ID in this field is correctly prefixed according to the NMDC Schema id_prefixes directives. In the example above, KO:K12960 is translated to KEGG.OTHOLOGY:K12960 to make sure the data is compliant with the registered prefix authorities and thus the NMDC Schema. This helps to ensure that the data is interoperable and can be used in a variety of tools and services beyond NMDC.
In 2023 NMDC transitioned from reusing identifiers from other organizations to using NMDC minted identifiers as the primary identifier.
"},{"location":"identifiers/#identifier-mapping","title":"Identifier mapping","text":"Identifier Example NMDC Schema Class NMDC Schema Slot gold:Gs* gold:Gs0114675 Study gold_study_identifiers gold:Gb* gold:Gb0110739 Biosample gold_biosample_identifiers emsl:* emsl:63ca2f94-6647-11eb-ae93-0242ac130002 Biosample emsl_biosample_identifiers igsn:* igsn:IEWFS001H Biosample igsn_biosample_identifiers gold:Gp* gold:Gp0452734 OmicsProcessing gold_sequencing_project_identifiers emsl:* emsl:598506 OmicsProcessing alternative_identifiersSome legacy data object identifiers were based on file md5sums, either with or without a prefix (nmdc, jgi, emsl). In some cases the legacy value can be found by removing the prefix and searching DataObject records on slot md5_checksum. If you are having trouble finding information based on legacy identifiers please contact support@microbiomedata.org.
"},{"location":"identifiers/#additional-details-on-legacy-identifiers","title":"Additional details on legacy identifiers","text":"Legacy metagenomics objects look like this:
id: \"gold:Gp0108335\"\n name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n has_input:\n - \"gold:Gb0108335\"\n part_of:\n - \"gold:Gs0112340\"\n has_output:\n - \"jgi:551a20d30d878525404e90d5\"\n omics_type: Metagenome\n type: \"nmdc:OmicsProcessing\"\n add_date: \"30-OCT-14 12.00.00.000000000 AM\"\n mod_date: \"22-MAY-20 06.13.12.927000000 PM\"\n ncbi_project_name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n processing_institution: \"Joint Genome Institute\"\n principal_investigator_name: \"Virginia Rich\"\nthe linked data object uses a jgi prefix and an md5 hash
id: \"jgi:551a20d30d878525404e90d5\"\n name: \"8871.1.114459.GCCAAT.fastq.gz\"\n description: \"Raw sequencer read data\"\n file_size_bytes: 17586370657\n type: \"nmdc:DataObject\"\nLegacy metaproteomics objects look like this:
id: \"emsl:404590\"\n name: \"FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n description: \"High res MS with low res CID MSn\"\n part_of:\n - \"gold:Gs0110132\"\n has_output:\n - \"emsl:output_404590\"\n omics_type: Proteomics\n type: \"nmdc:OmicsProcessing\"\n instrument_name: \"VOrbiETD03\"\n processing_institution: \"Environmental Molecular Sciences Lab\"\nand the output data objects are formed from these:
id: \"emsl:output_404590\"\n name: \"output: FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n description: \"High res MS with low res CID MSn\"\n file_size_bytes: 503296678\n type: \"nmdc:DataObject\"\nthe data objects use hashes (md5) prefixed with nmdc:
name: \"404590_resultant.tsv\"\n description: \"Aggregation of analysis tools{MSGFplus, MASIC} results\"\n file_size_bytes: 10948480\n type: \"nmdc:DataObject\"\n id: \"nmdc:e0c70280a7a23c7c5cc1e589f72e896e\"\nWe are working with the GSC to provide permanent IDs for MIxS terms. Note these terms are schema-level rather than data-level. For now we place these in the NMDC namespaces, e.g nmdc:alt
Using LinkML's default tooling, we produce a JSON-LD context with the schema:
When this is combined with schema-conformant JSON, RDF can be automatically created using the intended URIs
Please see: Maintaining identifiers] for more information on developing and maintaining identifiers in the schema.
"},{"location":"igsn_biosample_identifiers/","title":"Slot: IGSN Biosample Identifiers (igsn_biosample_identifiers)","text":"A list of identifiers for the biosample from the IGSN database.
URI: nmdc:igsn_biosample_identifiers
"},{"location":"igsn_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: igsn_biosample_identifiers\ndescription: A list of identifiers for the biosample from the IGSN database.\ntitle: IGSN Biosample Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- igsn_identifiers\nalias: igsn_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:igsn_identifiers
"},{"location":"igsn_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database None Biosample"},{"location":"igsn_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: igsn_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: igsn_identifiers\nrange: string\n\nA list of identifiers that relate the biosample to records in the IMG database.
URI: nmdc:img_identifiers
"},{"location":"img_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$
name: img_identifiers\ndescription: A list of identifiers that relate the biosample to records in the IMG\n database.\ntitle: IMG Identifiers\ntodos:\n- add is_a or mixin modeling, like other external_database_identifiers\n- what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nalias: img_identifiers\ndomain_of:\n- MetagenomeAnnotation\n- Biosample\n- MetatranscriptomeAnnotation\n- MetatranscriptomeExpressionAnalysis\n- MagsAnalysis\nrange: external_identifier\nmultivalued: true\npattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n\none or more combinations of other DataObjects that can be analyzed together
URI: nmdc:in_manifest
"},{"location":"in_manifest/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"in_manifest/#properties","title":"Properties","text":"Range: Manifest
Multivalued: True
name: in_manifest\ndescription: one or more combinations of other DataObjects that can be analyzed together\ncomments:\n- A DataObject can be part of multiple manifests, for example, a DataObject could\n be part of a manifest for a single run of an instrument and a manifest for technical\n replicates of a single sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: in_manifest\ndomain_of:\n- DataObject\nrange: Manifest\nmultivalued: true\nstructured_pattern:\n syntax: ^{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$\n interpolated: true\n\nURI: nmdc:inchi
"},{"location":"inchi/#properties","title":"Properties","text":"name: inchi\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi\nrange: string\n\nURI: nmdc:inchi_key
"},{"location":"inchi_key/#properties","title":"Properties","text":"name: inchi_key\nnotes:\n- 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n testing. J Cheminform. 4:12'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi_key\nrange: string\n\nA distinguishable space within a structure, the purpose for which discrete areas of a building is used
URI: MIXS:0000763
"},{"location":"indoor_space/#inheritance","title":"Inheritance","text":"name: indoor_space\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A distinguishable space within a structure, the purpose for which discrete\n areas of a building is used\ntitle: indoor space\nexamples:\n- value: foyer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor space\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000763\nalias: indoor_space\ndomain_of:\n- Biosample\nrange: indoor_space_enum\nmultivalued: false\n\nType of indoor surface
URI: MIXS:0000764
"},{"location":"indoor_surf/#inheritance","title":"Inheritance","text":"name: indoor_surf\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Type of indoor surface\ntitle: indoor surface\nexamples:\n- value: wall\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor surface\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000764\nalias: indoor_surf\ndomain_of:\n- Biosample\nrange: indoor_surf_enum\nmultivalued: false\n\nPercentage of industrial effluents received by wastewater treatment plant
URI: MIXS:0000662
"},{"location":"indust_eff_percent/#inheritance","title":"Inheritance","text":"name: indust_eff_percent\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Percentage of industrial effluents received by wastewater treatment plant\ntitle: industrial effluent percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- industrial effluent percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000662\nalias: indust_eff_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe amount of time it takes to complete each infiltration activity
URI: nmdc:infiltrations
"},{"location":"infiltrations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"infiltrations/#properties","title":"Properties","text":"Range: String
Multivalued: True
Regex pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$
name: infiltrations\ndescription: The amount of time it takes to complete each infiltration activity\nexamples:\n- value: '[''00:01:32'', ''00:00:53'']'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1\naliases:\n- infiltration_1\n- infiltration_2\nrank: 1000\nlist_elements_ordered: true\nalias: infiltrations\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\npattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$\n\nConcentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles
URI: MIXS:0000664
"},{"location":"inorg_particles/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: inorg_particles\nannotations:\n expected_value:\n tag: expected_value\n value: inorganic particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of particles such as sand, grit, metal particles, ceramics,\n etc.; can include multiple particles\ntitle: inorganic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inorganic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000664\nalias: inorg_particles\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe nucleotide base count number of input reads for QC analysis.
URI: nmdc:input_base_count
"},{"location":"input_base_count/#inheritance","title":"Inheritance","text":"name: input_base_count\ndescription: The nucleotide base count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_base_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nTotal number of input contigs.
URI: nmdc:input_contig_num
"},{"location":"input_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"input_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: input_contig_num\ndescription: Total number of input contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nTotal mass of sample used in activity.
URI: nmdc:input_mass
"},{"location":"input_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"input_mass/#properties","title":"Properties","text":"name: input_mass\ndescription: Total mass of sample used in activity.\ntitle: sample mass used\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample mass\n- sample weight\nexact_mappings:\n- MS:1000004\nnarrow_mappings:\n- MIXS:0000111\nrank: 1000\nalias: input_mass\ndomain_of:\n- Extraction\nrange: QuantityValue\n\n_TODO _
URI: nmdc:input_read_bases
"},{"location":"input_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_read_bases/#properties","title":"Properties","text":"name: input_read_bases\ndescription: 'TODO '\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_read_bases\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nThe sequence count number of input reads for QC analysis.
URI: nmdc:input_read_count
"},{"location":"input_read_count/#inheritance","title":"Inheritance","text":"name: input_read_count\ndescription: The sequence count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_read_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nThe volume of the input sample.
URI: nmdc:input_volume
"},{"location":"input_volume/#properties","title":"Properties","text":"name: input_volume\ndescription: The volume of the input sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_volume\nrange: QuantityValue\n\nURI: nmdc:insdc_analysis_identifiers
"},{"location":"insdc_analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$
name: insdc_analysis_identifiers\ncomments:\n- in INSDC this is a run but it corresponds to a GOLD analysis\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/runs/DRR218479\n description: Illumina MiSeq paired end sequencing of SAMD00212331\n- value: https://www.ebi.ac.uk/ena/browser/view/ERR436051\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$\n\nURI: nmdc:insdc_assembly_identifiers
"},{"location":"insdc_assembly_identifiers/#inheritance","title":"Inheritance","text":"Range: String
Regex pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$
name: insdc_assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: assembly_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_assembly_identifiers\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: string\npattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n\nidentifiers for corresponding project in INSDC Bioproject
URI: nmdc:insdc_bioproject_identifiers
"},{"location":"insdc_bioproject_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$
name: insdc_bioproject_identifiers\ndescription: identifiers for corresponding project in INSDC Bioproject\ncomments:\n- these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n one to one\nexamples:\n- value: https://bioregistry.io/bioproject:PRJNA366857\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ncbi.nlm.nih.gov/bioproject/\n- https://www.ddbj.nig.ac.jp/bioproject/index-e.html\naliases:\n- NCBI bioproject identifiers\n- DDBJ bioproject identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_bioproject_identifiers\ndomain_of:\n- NucleotideSequencing\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n\nidentifiers for corresponding sample in INSDC
URI: nmdc:insdc_biosample_identifiers
"},{"location":"insdc_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$
name: insdc_biosample_identifiers\ndescription: identifiers for corresponding sample in INSDC\nexamples:\n- value: https://bioregistry.io/biosample:SAMEA5989477\n- value: https://bioregistry.io/biosample:SAMD00212331\n description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/108\n- https://www.ebi.ac.uk/biosamples/\n- https://www.ncbi.nlm.nih.gov/biosample\n- https://www.ddbj.nig.ac.jp/biosample/index-e.html\naliases:\n- EBI biosample identifiers\n- NCBI biosample identifiers\n- DDBJ biosample identifiers\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n\nURI: nmdc:insdc_experiment_identifiers
"},{"location":"insdc_experiment_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$
name: insdc_experiment_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_experiment_identifiers\ndomain_of:\n- NucleotideSequencing\n- DataObject\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n\nAny identifier covered by the International Nucleotide Sequence Database Collaboration
URI: nmdc:insdc_identifiers
"},{"location":"insdc_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA None insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject None Study, NucleotideSequencing insdc_biosample_identifiers identifiers for corresponding sample in INSDC None Biosample insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC None insdc_experiment_identifiers None DataObject, NucleotideSequencing insdc_analysis_identifiers None insdc_assembly_identifiers None MetatranscriptomeAssembly, MetagenomeAssembly"},{"location":"insdc_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: insdc_identifiers\ndescription: Any identifier covered by the International Nucleotide Sequence Database\n Collaboration\ncomments:\n- note that we deliberately abstract over which of the partner databases accepted\n the initial submission\n- 'the first letter of the accession indicates which partner accepted the initial\n submission: E for ENA, D for DDBJ, or S or N for NCBI.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.insdc.org/\n- https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html\naliases:\n- EBI identifiers\n- NCBI identifiers\n- DDBJ identifiers\nrank: 1000\nmixin: true\nalias: insdc_identifiers\nrange: string\n\nsecondary identifiers for corresponding sample in INSDC
URI: nmdc:insdc_secondary_sample_identifiers
"},{"location":"insdc_secondary_sample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^biosample:(E|D|S)RS[0-9]{6,}$
name: insdc_secondary_sample_identifiers\ndescription: secondary identifiers for corresponding sample in INSDC\ncomments:\n- ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340\n -> SAMD00212331\n- MGnify uses these as their primary sample IDs\nexamples:\n- value: https://bioregistry.io/insdc.sra:DRS166340\n description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_secondary_sample_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^biosample:(E|D|S)RS[0-9]{6,}$\n\nidentifiers for corresponding project in INSDC SRA / ENA
URI: nmdc:insdc_sra_ena_study_identifiers
"},{"location":"insdc_sra_ena_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$
name: insdc_sra_ena_study_identifiers\ndescription: identifiers for corresponding project in INSDC SRA / ENA\nexamples:\n- value: https://bioregistry.io/insdc.sra:SRP121659\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/109\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\naliases:\n- EBI ENA study identifiers\n- NCBI SRA identifiers\n- DDBJ SRA identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_sra_ena_study_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$\n\nThe recorded value at sampling time (power density)
URI: MIXS:0000168
"},{"location":"inside_lux/#inheritance","title":"Inheritance","text":"name: inside_lux\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatt per square metre\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded value at sampling time (power density)\ntitle: inside lux light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inside lux light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000168\nalias: inside_lux\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThis property links a database object to the set of instruments within it.
URI: nmdc:instrument_set
"},{"location":"instrument_set/#inheritance","title":"Inheritance","text":"Range: Instrument
Multivalued: True
name: instrument_set\ndescription: This property links a database object to the set of instruments within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: instrument_set\ndomain_of:\n- Database\nrange: Instrument\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nWhat instrument was used during DataGeneration or MaterialProcessing.
URI: nmdc:instrument_used
"},{"location":"instrument_used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no FiltrationProcess The process of segregation of phases; e no LibraryPreparation no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no Pooling physical combination of several instances of like material no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no"},{"location":"instrument_used/#properties","title":"Properties","text":"Range: Instrument
Multivalued: True
name: instrument_used\ndescription: What instrument was used during DataGeneration or MaterialProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: instrument_used\ndomain_of:\n- MaterialProcessing\n- DataGeneration\nrange: Instrument\nmultivalued: true\n\nThe physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000813
"},{"location":"int_wall_cond/#inheritance","title":"Inheritance","text":"name: int_wall_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the wall at the time of sampling; photos or\n video preferred; use drawings to indicate location of damaged areas\ntitle: interior wall condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- interior wall condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000813\nalias: int_wall_cond\ndomain_of:\n- Biosample\nrange: int_wall_cond_enum\nmultivalued: false\n\nwhether internal calibration was used, if false, external calibration was used
URI: nmdc:internal_calibration
"},{"location":"internal_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process yes"},{"location":"internal_calibration/#properties","title":"Properties","text":"name: internal_calibration\ndescription: whether internal calibration was used, if false, external calibration\n was used\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: internal_calibration\ndomain_of:\n- CalibrationInformation\nrange: boolean\n\nfield describing aspect of the investigation/study to which the sample belongs
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:investigation_field
"},{"location":"investigation_field/#inheritance","title":"Inheritance","text":"name: investigation field\ndescription: field describing aspect of the investigation/study to which the sample\n belongs\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: investigation_field\ndomain_of:\n- Biosample\nrange: string\n\nThe ionization source used to introduce processed samples into a mass spectrometer
URI: nmdc:ionization_source
"},{"location":"ionization_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"ionization_source/#properties","title":"Properties","text":"name: ionization_source\ndescription: The ionization source used to introduce processed samples into a mass\n spectrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1000008\nrank: 1000\nalias: ionization_source\ndomain_of:\n- MassSpectrometryConfiguration\nrange: IonizationSourceEnum\n\nWhether or not pressure was applied to a thing or process.
URI: nmdc:is_pressurized
"},{"location":"is_pressurized/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"is_pressurized/#properties","title":"Properties","text":"name: is_pressurized\ndescription: Whether or not pressure was applied to a thing or process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_pressurized\ndomain_of:\n- FiltrationProcess\nrange: boolean\n\nIs the (RNA) library stranded or non-stranded (unstranded).
URI: nmdc:is_stranded
"},{"location":"is_stranded/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"is_stranded/#properties","title":"Properties","text":"name: is_stranded\ndescription: Is the (RNA) library stranded or non-stranded (unstranded).\ncomments:\n- A value of true means the library is stranded, flase means non-stranded.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_stranded\ndomain_of:\n- LibraryPreparation\nrange: boolean\n\nList isotope exposure or addition applied to your sample.
URI: nmdc:isotope_exposure
"},{"location":"isotope_exposure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"isotope_exposure/#properties","title":"Properties","text":"Range: String
Recommended: True
name: isotope_exposure\ndescription: List isotope exposure or addition applied to your sample.\ntitle: isotope exposure/addition\ntodos:\n- Can we make the H218O correctly super and subscripted?\ncomments:\n- This is required when your experimental design includes the use of isotopically\n labeled compounds\nexamples:\n- value: 13C glucose\n- value: 18O water\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000751\nrank: 16\nalias: isotope_exposure\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nInjection water breakthrough date per well following a secondary and/or tertiary recovery
URI: MIXS:0001010
"},{"location":"iw_bt_date_well/#inheritance","title":"Inheritance","text":"name: iw_bt_date_well\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Injection water breakthrough date per well following a secondary and/or\n tertiary recovery\ntitle: injection water breakthrough date of specific well\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water breakthrough date of specific well\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001010\nalias: iw_bt_date_well\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nProportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)
URI: MIXS:0000455
"},{"location":"iwf/#inheritance","title":"Inheritance","text":"name: iwf\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Proportion of the produced fluids derived from injected water at the\n time of sampling. (e.g. 87%)\ntitle: injection water fraction\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water fraction\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000455\nalias: iwf\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nidentifiers for corresponding analysis projects in JGI Portal
URI: nmdc:jgi_portal_analysis_project_identifiers
"},{"location":"jgi_portal_analysis_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^jgi.analysis:[0-9]+$
Instances of this class should have identifiers with one of the following prefixes:
name: jgi_portal_analysis_project_identifiers\nid_prefixes:\n- jgi.analysis\ndescription: identifiers for corresponding analysis projects in JGI Portal\nexamples:\n- value: https://data.jgi.doe.gov/search?q=1414320\n description: Metagenome - Draft Assembly YELL_051-M-20210705-comp-DNA1\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- jgi_portal_identifiers\nalias: jgi_portal_analysis_project_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^jgi.analysis:[0-9]+$\n\nidentifiers for entities according to JGI Portal
URI: nmdc:jgi_portal_identifiers
"},{"location":"jgi_portal_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... None Study jgi_portal_analysis_project_identifiers identifiers for corresponding analysis projects in JGI Portal None"},{"location":"jgi_portal_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: jgi_portal_identifiers\ndescription: identifiers for entities according to JGI Portal\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://data.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: jgi_portal_identifiers\nrange: string\n\nIdentifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier.
URI: nmdc:jgi_portal_study_identifiers
"},{"location":"jgi_portal_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^jgi.proposal:\\d+$
Instances of this class should have identifiers with one of the following prefixes:
name: jgi_portal_study_identifiers\nid_prefixes:\n- jgi.proposal\ndescription: Identifiers that link a NMDC study to a website hosting raw and analyzed\n data for a JGI proposal. The suffix of the curie can used to query the GOLD API\n and is interoperable with an award DOI from OSTI and a GOLD study identifier.\ntitle: JGI Portal Study identifiers\ncomments:\n- Could this could be considered a related identifier?\n- Curie suffix is the Site Award Number from an OSTI award page\n- Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD study\n identifier gold:Gs0154044\n- bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\nexamples:\n- value: jgi.proposal:507130\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- jgi_portal_identifiers\nalias: jgi_portal_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^jgi.proposal:\\d+$\n\nThe substance from which a portion was taken.
URI: nmdc:known_as
"},{"location":"known_as/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"known_as/#properties","title":"Properties","text":"name: known_as\ndescription: The substance from which a portion was taken.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: known_as\ndomain_of:\n- PortionOfSubstance\nrange: ChemicalEntityEnum\n\nShould use ISO 639-1 code e.g. \"en\", \"fr\"
URI: nmdc:language
"},{"location":"language/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextValue A basic string value no"},{"location":"language/#properties","title":"Properties","text":"name: language\ndescription: Should use ISO 639-1 code e.g. \"en\", \"fr\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: language\ndomain_of:\n- TextValue\nrange: language_code\n\nThe last time the floor was cleaned (swept, mopped, vacuumed)
URI: MIXS:0000814
"},{"location":"last_clean/#inheritance","title":"Inheritance","text":"name: last_clean\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The last time the floor was cleaned (swept, mopped, vacuumed)\ntitle: last time swept/mopped/vacuumed\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- last time swept/mopped/vacuumed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000814\nalias: last_clean\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system
URI: MIXS:0000009
"},{"location":"lat_lon/#inheritance","title":"Inheritance","text":"name: lat_lon\nannotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\ndescription: The geographical origin of the sample as defined by latitude and longitude.\n The values should be reported in decimal degrees and in WGS84 system\ntitle: geographic location (latitude and longitude)\nexamples:\n- value: 50.586825 6.408977\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (latitude and longitude)\nrank: 1000\nis_a: environment field\nstring_serialization: '{float} {float}'\nslot_uri: MIXS:0000009\nalias: lat_lon\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: GeolocationValue\nmultivalued: false\n\nlatitude
URI: wgs84:lat
"},{"location":"latitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"latitude/#properties","title":"Properties","text":"name: latitude\ndescription: latitude\nexamples:\n- value: '-33.460524'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:latitude\nrank: 1000\nslot_uri: wgs84:lat\nalias: latitude\ndomain_of:\n- GeolocationValue\nrange: decimal_degree\n\nlime buffer capacity, determined after 30 minute incubation
URI: nmdc:lbc_thirty
"},{"location":"lbc_thirty/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lbc_thirty/#properties","title":"Properties","text":"name: lbc_thirty\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\ndescription: lime buffer capacity, determined after 30 minute incubation\ntitle: lime buffer capacity (at 30 minutes)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n pH unit\nexamples:\n- value: 543 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\n- https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\naliases:\n- lbc_thirty\n- lbc30\n- lime buffer capacity (at 30 minutes)\nrank: 1000\nalias: lbc_thirty\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nlime buffer capacity, determined at equilibrium after 5 day incubation
URI: nmdc:lbceq
"},{"location":"lbceq/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lbceq/#properties","title":"Properties","text":"name: lbceq\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\ndescription: lime buffer capacity, determined at equilibrium after 5 day incubation\ntitle: lime buffer capacity (after 5 day incubation)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n pH unit\nexamples:\n- value: 1575 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- lbceq\n- lime buffer capacity (at 5-day equilibrium)\nrank: 1000\nalias: lbceq\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:library_preparation_kit
"},{"location":"library_preparation_kit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_preparation_kit/#properties","title":"Properties","text":"name: library_preparation_kit\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_preparation_kit\ndomain_of:\n- LibraryPreparation\nrange: string\n\nURI: nmdc:library_type
"},{"location":"library_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_type/#properties","title":"Properties","text":"name: library_type\ntitle: library type\nexamples:\n- value: DNA\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_type\ndomain_of:\n- LibraryPreparation\nrange: LibraryTypeEnum\n\nMeasurement of light intensity
URI: MIXS:0000706
"},{"location":"light_intensity/#inheritance","title":"Inheritance","text":"name: light_intensity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of light intensity\ntitle: light intensity\nexamples:\n- value: 0.3 lux\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light intensity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000706\nalias: light_intensity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment(s) involving exposure to light, including both light intensity and quality.
URI: MIXS:0000569
"},{"location":"light_regm/#inheritance","title":"Inheritance","text":"name: light_regm\nannotations:\n expected_value:\n tag: expected_value\n value: exposure type;light intensity;light quality\n preferred_unit:\n tag: preferred_unit\n value: lux; micrometer, nanometer, angstrom\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about treatment(s) involving exposure to light, including\n both light intensity and quality.\ntitle: light regimen\nexamples:\n- value: incandescant light;10 lux;450 nanometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000569\nalias: light_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nApplication of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light
URI: MIXS:0000769
"},{"location":"light_type/#inheritance","title":"Inheritance","text":"Range: LightTypeEnum
Multivalued: True
name: light_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Application of light to achieve some practical or aesthetic effect. Lighting\n includes the use of both artificial light sources such as lamps and light fixtures,\n as well as natural illumination by capturing daylight. Can also include absence\n of light\ntitle: light type\nexamples:\n- value: desk lamp\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000769\nalias: light_type\ndomain_of:\n- Biosample\nrange: light_type_enum\nmultivalued: true\n\nLink to additional analysis results performed on the sample
URI: MIXS:0000340
"},{"location":"link_addit_analys/#inheritance","title":"Inheritance","text":"name: link_addit_analys\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to additional analysis results performed on the sample\ntitle: links to additional analysis\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- links to additional analysis\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000340\nalias: link_addit_analys\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nLink to digitized soil maps or other soil classification information
URI: MIXS:0000329
"},{"location":"link_class_info/#inheritance","title":"Inheritance","text":"name: link_class_info\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to digitized soil maps or other soil classification information\ntitle: link to classification information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to classification information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000329\nalias: link_class_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nLink to climate resource
URI: MIXS:0000328
"},{"location":"link_climate_info/#inheritance","title":"Inheritance","text":"name: link_climate_info\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to climate resource\ntitle: link to climate information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to climate information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000328\nalias: link_climate_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nHydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000990
"},{"location":"lithology/#inheritance","title":"Inheritance","text":"name: lithology\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: lithology\nexamples:\n- value: Volcanic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000990\nalias: lithology\ndomain_of:\n- Biosample\nrange: lithology_enum\nmultivalued: false\n\nSoil classification based on local soil classification system
URI: MIXS:0000330
"},{"location":"local_class/#inheritance","title":"Inheritance","text":"name: local_class\nannotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Soil classification based on local soil classification system\ntitle: soil_taxonomic/local classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000330\nalias: local_class\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\nReference or method used in determining the local soil classification
URI: MIXS:0000331
"},{"location":"local_class_meth/#inheritance","title":"Inheritance","text":"name: local_class_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the local soil classification\ntitle: soil_taxonomic/local classification method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000331\nalias: local_class_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:location
"},{"location":"location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"location/#properties","title":"Properties","text":"name: location\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: location\ndomain_of:\n- Biosample\nrange: string\n\nlongitude
URI: wgs84:long
"},{"location":"longitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"longitude/#properties","title":"Properties","text":"name: longitude\ndescription: longitude\nexamples:\n- value: '150.168149'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:longitude\nrank: 1000\nslot_uri: wgs84:long\nalias: longitude\ndomain_of:\n- GeolocationValue\nrange: decimal_degree\n\nNumber of contigs which were excluded from binning for depth of coverage.
URI: nmdc:low_depth_contig_num
"},{"location":"low_depth_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"low_depth_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: low_depth_contig_num\ndescription: Number of contigs which were excluded from binning for depth of coverage.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: low_depth_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nConcentration of magnesium in the sample
URI: MIXS:0000431
"},{"location":"magnesium/#inheritance","title":"Inheritance","text":"name: magnesium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter, parts per million, micromole per kilogram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of magnesium in the sample\ntitle: magnesium\nexamples:\n- value: 52.8 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- magnesium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000431\nalias: magnesium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nContains detailed information about each metagenome-assembled genome.
URI: nmdc:mags_list
"},{"location":"mags_list/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"mags_list/#properties","title":"Properties","text":"Range: MagBin
Multivalued: True
name: mags_list\ndescription: Contains detailed information about each metagenome-assembled genome.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mags_list\ndomain_of:\n- MagsAnalysis\nrange: MagBin\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe nmdc-schema is a framework for describing multi-omics microbiome experiments and the data they produce. We aim to answer questions like:
All metadata gathered and stored by the NMDC community must validate against the NMDC Schema.
"},{"location":"maintaining-the-schema/#the-nmdc-schema-is-expressed-in-the-linkml-modeling-language","title":"The NMDC Schema is expressed in the LinkML modeling language.","text":"LinkML uses structures like classes, slots (for relationships and properties), types and enumerations to create a blueprint of the NMDC data. The schema is used to define the structure of the data, and to ensure that the data is consistent and interoperable. The schema is expressed in a human-readable format, and with the help of LinkML tooling, can be generated in multiple formats, including JSONSchema (used to support validation on ingest to NMDC), YAML (for ease of editing), and OWL. LinkML schemas generally make good use of terminology and concepts already modeled in external, trusted knowledge centers, especially ontologies, and especially those from the OBO Foundry.
Reuse of existing terminologies and knowledge can be found in several places in the NMDC schema, including the use of the MIxS schema, the EnvO ontology, and the CHEBI ontology. In addition, the NMDC schema elements like slots and classes are annotated with mappings (exact, narrow, related scopes) to these external resources.
For example:
doi_value:\n description: >-\n A digital object identifier, which is intended to persistantly identify some resource on the web.\n required: true\n aliases:\n - DOI\n - digital object identifier\n range: uriorcurie\n pattern: '^doi:10.\\d{2,9}/.*$'\n examples:\n - value: doi:10.46936/10.25585/60000880\n description: The DOI links to an electronic document.\n exact_mappings:\n - OBI:0002110\n narrow_mappings:\n - edam.data:1188\nOne consequence of this semantic/linked data orientation is that all schema elements are identified by a URI, most often in the compact CURIe form: a prefix and a local identifier. Even if a class isn't decorated with a class_uri annotation, it will always have a key (in a JSON, YAML or Python Obj sense), which is sometimes reiterated as the name. In that case, the class' URI will be <prefix>:<key>. LinkML schemas should have default prefix assertions, but any element can use a different prefix, as long as an expansion is provided.
Prefixes used in a LinkML must be associated with an expansion in the schema (which may include imported modules). Ideally, the expanded URI should be web resolvable, but that is not required. The prefixes can be expanded to base URIs owned by a particular resource, or they can be expanded to base URIs owned by some resolving service, like the bioregistry.
"},{"location":"maintaining-the-schema/#asserting-mappings-in-the-nmdc-schema","title":"Asserting mappings in the NMDC Schema","text":"As mentioned above, URIs are assigned to most elements of a LinkML schema, either explicitly by the schema authors, or implicitly through the default prefix and the element's key. If an external prefix is used, that means the semantics of the element are identical to the external term, unless otherwise refined. Sometimes it is desirable to associate a LinkML schema element with a term from an external resource, without asserting that the semantics are identical. In this case, a variety of mapping terms can be used.
Adding mappings to a schema element is one of the best and most compact ways to clarify the meaning of that element.
Schema contributors are strongly encouraged to use mappings whose prefixes are already defined in the schema. Schema contributors are always responsible for having a holistic understanding of an external term to be mapped into the schema. This means gaining familiarity with the parent and child terms, as well as any other axioms applied to the term. The EBI Ontology Lookup Service is a good place to look for these details.
When it appears necessary to use a mapping whose prefix isn't already defined in the schema, the contributor is responsible for having a holistic understanding of the external namespace (not just the term to be mapped). There are several ways to start assessing an ontology that is being considered as a source of mappings. If the ontology is in the OBO Foundry, one can look at the OBO Foundry Dashboard.
"},{"location":"maintaining-the-schema/#asserting-identifiers-in-linkml-data","title":"Asserting identifiers in LinkML data","text":"Generally speaking, the smallest atom of LinkML data is an instance of one class. LinkML slots take values, but always in the context of some class (on the right hand side). LinkML data files are frequently collections of instances of one or more classes. The is no requirement that these classes provide a slot whose value uniquely identifies the instances, but LinkML provides a mechanism that is broadly followed: one slot available in each class is annotated with identifier: true. (Or at least, that's what it would look like in a YAML serialization.) That means that the slot is required in all instances of the class, and that any collection of instances from that class must have unique values in that slot. It is also typical to say that the range of the is type uriorcurie.
A common pattern in the nmdc-schema is asserting that some identifiable process has inputs and outputs.
pooling_set:\n - id: pooling:1\n inputs:\n - biosample:1\n - biosample:2\n - biosample:3\n - id: pooling:2\n inputs:\n - biosample:4\n - biosample:5\n - biosample:6\nHere we have declared the existence of two pooling processes. A CURIe identifier is asserted for both of them, and three inputs are mentioned for each. The example CURIes above don't necessarily follow any nmdc-schema identifier pattern rules. If these were real CURIes, then the pooling and biosample prefixes would have to be defined in the schema files.
In this case, let's assume definitions for the biosample inputs should be defined elsewhere in an NMDC data set. Cases in which biosamples are mentioned without being defined would be considered violations of the referential integrity. The development of referential integrity validators for LinkML has begun in Autumn, 2023.
Another pattern is saying that something defined within a NMDC data set is equivalent to something defined elsewhere.
biosample_set:\n - id: biosample:1\n gold_biosample_identifiers:\n - gold:1\n - gold:2\nIn this case, the gold prefix must be defined in the schema. When expanded to URIs via the prefix definitions, these gold_biosample_identifiers would all be web-resolvable.
"},{"location":"maintaining-the-schema/#constraining-mentioned-identifiers","title":"Constraining mentioned identifiers","text":"We can limit the values that go into any slot by using a pattern constraint. We can also use the id_prefixes constraint to limit the prefixes that are used in whatever slot has been declared to be the identifier of a class. (Attributes of a class are supposed to be cascaded to subclasses, via the is_a attribute. This may not always be the case though. In the nmdc-schema we have been using a belt-and-suspenders approach of re-declaring the uriorcurie range )
All prefixes used in the id_prefixes constraint must be defined in the schema. We should have a standing practice of reflecting on the declared id_prefixes, and removing prefixes that haven't been used yet and are not likely to eer be used.
Maintenance of the prefix portions of a pattern will generally require more manual checking. We shouldn't be constraining the values of slots to use a prefix that isn't declared, but no checks are automatically applied.
Any class could use any slot with any range to \"link to\" something external. A Person could have a place_of_birth slot, and that could take unconstrained string or enumerated values like \"Switzerland\". But that doesn't provide much support for people looking up more information about the place_of_birth. You could create wikidata_place_of_birth and dbpedia_place_of_birth slots and add annotations to the slot to aid in external lookups, but that isn't a good practice if supporting several external targets. A better practice is to have one place_of_birth slot, with the uriorcuire range. Then users can provide values like <http://www.wikidata.org/entity/Q39> or <http://dbpedia.org/resource/Switzerland>. Then there is no ambiguity about the target of the link.
If the schema contains prefix definitions like wd: <http://www.wikidata.org/entity/> and dbpedia: <http://dbpedia.org/resource/>, then the values can be written as wd:Q39 and dbpedia:Switzerland. This is more compact and readable, but it requires that the prefixes be defined in the schema. Then, more constraint can be imposed with a pattern on the place_of_birth slot like '^(wd|dbpedia):.+$'
make gen-project)default_curi_maps any more--emsl-biosample-uuid-replacement in anyuri-strings-to-irispatterns and id_prefixeswarning Schema maps prefix 'CHEMBL.COMPOUND' to namespace 'https://bioregistry.io/chembl.compound:' instead of namespace 'http://identifiers.org/chembl.compound/' (canonical_prefixes)
warning Schema maps prefix 'rdf' to namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' instead of using prefix ' RDF' (canonical_prefixes) warning Schema maps prefix 'rdfs' to namespace 'http://www.w3.org/2000/01/rdf-schema#' instead of using prefix 'RDFS' ( canonical_prefixes)
"},{"location":"maintaining-the-schema/#typecodes","title":"Typecodes","text":"Not only does NMDC require the use of the nmdc prefix in the primary identifier for data instances, but we also define a pattern that the local portion of the ids must follow. For example, an example id from the NamedThing class is 'nmdc:mgmag-00-x012.1_7_c1'. The text that comes immediately after the nmdc prefix and colon, and before the first hyphen is the typecode, mgmag in this case. Typecodes must correspond 1:1 to a class in the NMDC schema. The typecodes currently in use are available from the nmdc-runtime API: https://api.microbiomedata.org/nmdcschema/typecodes
Please see identifers for more information on the minting of identifiers in NMDC directly, and for more discussion on identifier resolution and harmonization in NMDC.
"},{"location":"manganese/","title":"Slot: manganese (manganese)","text":"Concentration of manganese in the sample
URI: nmdc:manganese
"},{"location":"manganese/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"manganese/#properties","title":"Properties","text":"name: manganese\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of manganese in the sample\ntitle: manganese\nexamples:\n- value: 24.7 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- manganese\nrank: 1000\nalias: manganese\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of context in which the constituent DataObjects can be analyzed together.
URI: nmdc:manifest_category
"},{"location":"manifest_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Manifest A qualified collection of DataObjects that can be analyzed together in the sa... no"},{"location":"manifest_category/#properties","title":"Properties","text":"Range: ManifestCategoryEnum
Required: True
name: manifest_category\ndescription: The type of context in which the constituent DataObjects can be analyzed\n together.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: manifest_category\ndomain_of:\n- Manifest\nrange: ManifestCategoryEnum\nrequired: true\n\nThis property links a database object to the set of manifests within it.
URI: nmdc:manifest_set
"},{"location":"manifest_set/#inheritance","title":"Inheritance","text":"Range: Manifest
Multivalued: True
name: manifest_set\ndescription: This property links a database object to the set of manifests within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: manifest_set\ndomain_of:\n- Database\nrange: Manifest\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
URI: nmdc:mass
"},{"location":"mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"mass/#properties","title":"Properties","text":"name: mass\ndescription: A physical quality that inheres in a bearer by virtue of the proportion\n of the bearer's amount of matter.\ntitle: mass\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- PATO:0000125\nrank: 1000\nalias: mass\ndomain_of:\n- SubSamplingProcess\n- PortionOfSubstance\nrange: QuantityValue\n\nThe kind of mass analyzer(s) used during the spectra collection.
URI: nmdc:mass_analyzers
"},{"location":"mass_analyzers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_analyzers/#properties","title":"Properties","text":"Range: MassAnalyzerEnum
Multivalued: True
name: mass_analyzers\ndescription: The kind of mass analyzer(s) used during the spectra collection.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1000443\nrank: 1000\nalias: mass_analyzers\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassAnalyzerEnum\nmultivalued: true\n\nMode of running a mass spectrometer method by which m/z ranges are selected and ions possibly fragment.
URI: nmdc:mass_spectrometry_acquisition_strategy
"},{"location":"mass_spectrometry_acquisition_strategy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_spectrometry_acquisition_strategy/#properties","title":"Properties","text":"name: mass_spectrometry_acquisition_strategy\ndescription: Mode of running a mass spectrometer method by which m/z ranges are selected\n and ions possibly fragment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1003213\nrank: 1000\nalias: mass_spectrometry_acquisition_strategy\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassSpectrometryAcquisitionStrategyEnum\n\nIndicates whether mass spectra were collected in full profile, reduced profile, or centroid mode during acquisition.
URI: nmdc:mass_spectrum_collection_modes
"},{"location":"mass_spectrum_collection_modes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_spectrum_collection_modes/#properties","title":"Properties","text":"Range: MassSpectrumCollectionModeEnum
Multivalued: True
name: mass_spectrum_collection_modes\ndescription: Indicates whether mass spectra were collected in full profile, reduced\n profile, or centroid mode during acquisition.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mass_spectrum_collection_modes\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassSpectrumCollectionModeEnum\nmultivalued: true\n\nA material processing in which components of an input material become segregated in space
URI: nmdc:material_component_separation
"},{"location":"material_component_separation/#properties","title":"Properties","text":"name: material_component_separation\ndescription: A material processing in which components of an input material become\n segregated in space\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: material_component_separation\nrange: string\n\nThis property links a database object to the set of material processing within it.
URI: nmdc:material_processing_set
"},{"location":"material_processing_set/#inheritance","title":"Inheritance","text":"Range: MaterialProcessing
Multivalued: True
name: material_processing_set\ndescription: This property links a database object to the set of material processing\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: material_processing_set\ndomain_of:\n- Database\nrange: MaterialProcessing\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe maximum amount of people allowed in the indoor environment
URI: MIXS:0000229
"},{"location":"max_occup/#inheritance","title":"Inheritance","text":"name: max_occup\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The maximum amount of people allowed in the indoor environment\ntitle: maximum occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- maximum occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000229\nalias: max_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMD5 checksum of file (pre-compressed)
URI: nmdc:md5_checksum
"},{"location":"md5_checksum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"md5_checksum/#properties","title":"Properties","text":"name: md5_checksum\ndescription: MD5 checksum of file (pre-compressed)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: md5_checksum\ndomain_of:\n- DataObject\nrange: string\n\nMeasurement of mean friction velocity
URI: MIXS:0000498
"},{"location":"mean_frict_vel/#inheritance","title":"Inheritance","text":"name: mean_frict_vel\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of mean friction velocity\ntitle: mean friction velocity\nexamples:\n- value: 0.5 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000498\nalias: mean_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of mean peak friction velocity
URI: MIXS:0000502
"},{"location":"mean_peak_frict_vel/#inheritance","title":"Inheritance","text":"name: mean_peak_frict_vel\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of mean peak friction velocity\ntitle: mean peak friction velocity\nexamples:\n- value: 1 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean peak friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000502\nalias: mean_peak_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nmechanical structure: a moving structure
URI: MIXS:0000815
"},{"location":"mech_struc/#inheritance","title":"Inheritance","text":"name: mech_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'mechanical structure: a moving structure'\ntitle: mechanical structure\nexamples:\n- value: elevator\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000815\nalias: mech_struc\ndomain_of:\n- Biosample\nrange: mech_struc_enum\nmultivalued: false\n\nInformation about any mechanical damage exerted on the plant; can include multiple damages and sites
URI: MIXS:0001052
"},{"location":"mechanical_damage/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: mechanical_damage\nannotations:\n expected_value:\n tag: expected_value\n value: damage type;body site\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about any mechanical damage exerted on the plant; can include\n multiple damages and sites\ntitle: mechanical damage\nexamples:\n- value: pruning;bark\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical damage\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0001052\nalias: mechanical_damage\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nNames of the contigs that make up a metagenome-assembled genome.
URI: nmdc:members_id
"},{"location":"members_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"members_id/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: members_id\ndescription: Names of the contigs that make up a metagenome-assembled genome.\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- GENEPIO:0100596\nrank: 1000\nalias: members_id\ndomain_of:\n- MagBin\nrange: string\nmultivalued: true\n\nthe specific metabolite identifier
URI: nmdc:metabolite_identified
"},{"location":"metabolite_identified/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"metabolite_identified/#properties","title":"Properties","text":"name: metabolite_identified\ndescription: the specific metabolite identifier\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metabolite_identified\ndomain_of:\n- MetaboliteIdentification\nrange: string\n\nThe identifier for the analysis activity that generated the functional annotation results, where the analysis activity is an instance of the/an appropriate subclass of WorkflowExecution
URI: nmdc:metagenome_annotation_id
","text":""},{"location":"metagenome_annotation_id/#properties","title":"Properties","text":"Range: WorkflowExecution
Required: True
name: metagenome_annotation_id\ndescription: The identifier for the analysis activity that generated the functional\n annotation results, where the analysis activity is an instance of the/an appropriate\n subclass of WorkflowExecution\ndeprecated: not used. 2024-10 https://github.com/microbiomedata/nmdc-schema/issues/1253\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metagenome_annotation_id\nrange: WorkflowExecution\nrequired: true\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:metagenome_assembly_parameter
"},{"location":"metagenome_assembly_parameter/#inheritance","title":"Inheritance","text":"name: metagenome_assembly_parameter\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: metagenome_assembly_parameter\nrange: string\n\nThe category of metaproteomics analysis being performed.
URI: nmdc:metaproteomics_analysis_category
"},{"location":"metaproteomics_analysis_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no"},{"location":"metaproteomics_analysis_category/#properties","title":"Properties","text":"Range: MetaproteomicsAnalysisCategoryEnum
Required: True
name: metaproteomics_analysis_category\ndescription: The category of metaproteomics analysis being performed.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metaproteomics_analysis_category\ndomain_of:\n- MetaproteomicsAnalysis\nrange: MetaproteomicsAnalysisCategoryEnum\nrequired: true\n\nMethane (gas) amount or concentration at the time of sampling
URI: MIXS:0000101
"},{"location":"methane/#inheritance","title":"Inheritance","text":"name: methane\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per billion, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Methane (gas) amount or concentration at the time of sampling\ntitle: methane\nexamples:\n- value: 1800 parts per billion\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- methane\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000101\nalias: methane\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:mgnify_analysis_identifiers
"},{"location":"mgnify_analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: mgnify_analysis_identifiers\nnotes:\n- 'removed pattern: \"^mgnify:MGYA[0-9]+$\" ## TODO https://github.com/bioregistry/bioregistry/issues/109'\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270\n description: combined analyses (taxonomic, functional) of sample ERS438107\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- mgnify_identifiers\nalias: mgnify_analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:mgnify_identifiers
"},{"location":"mgnify_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain mgnify_project_identifiers identifiers for corresponding project in MGnify None Study mgnify_analysis_identifiers None"},{"location":"mgnify_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: mgnify_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ebi.ac.uk/metagenomics/\nrank: 1000\nmixin: true\nalias: mgnify_identifiers\nrange: string\n\nidentifiers for corresponding project in MGnify
URI: nmdc:mgnify_project_identifiers
"},{"location":"mgnify_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^mgnify.proj:[A-Z]+[0-9]+$
name: mgnify_project_identifiers\ndescription: identifiers for corresponding project in MGnify\nexamples:\n- value: https://bioregistry.io/mgnify.proj:MGYS00005757\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- mgnify_identifiers\nalias: mgnify_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^mgnify.proj:[A-Z]+[0-9]+$\n\nReference or method used in determining microbial biomass carbon
URI: nmdc:micro_biomass_c_meth
"},{"location":"micro_biomass_c_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_c_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: micro_biomass_c_meth\ndescription: Reference or method used in determining microbial biomass carbon\ntitle: microbial biomass carbon method\ntodos:\n- How should we separate values? | or ;? lets be consistent\ncomments:\n- required if \"microbial_biomass_c\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000339\nrank: 11\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_c_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nReference or method used in determining microbial biomass
URI: MIXS:0000339
"},{"location":"micro_biomass_meth/#inheritance","title":"Inheritance","text":"name: micro_biomass_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining microbial biomass\ntitle: microbial biomass method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000339\nalias: micro_biomass_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nReference or method used in determining microbial biomass nitrogen
URI: nmdc:micro_biomass_n_meth
"},{"location":"micro_biomass_n_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_n_meth/#properties","title":"Properties","text":"name: micro_biomass_n_meth\ndescription: Reference or method used in determining microbial biomass nitrogen\ntitle: microbial biomass nitrogen method\ncomments:\n- required if \"microbial_biomass_n\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000339\nrank: 13\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_n_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units
URI: MIXS:0000650
"},{"location":"microbial_biomass/#inheritance","title":"Inheritance","text":"name: microbial_biomass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram per kilogram soil\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer. If you keep this, you would need to have correction\n factors used for conversion to the final units\ntitle: microbial biomass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000650\nalias: microbial_biomass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.
URI: nmdc:microbial_biomass_c
"},{"location":"microbial_biomass_c/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_c/#properties","title":"Properties","text":"name: microbial_biomass_c\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer.\ntitle: microbial biomass carbon\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n method are required\nexamples:\n- value: 0.05 ug C/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 10\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_c\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.
URI: nmdc:microbial_biomass_n
"},{"location":"microbial_biomass_n/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_n/#properties","title":"Properties","text":"name: microbial_biomass_n\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer.\ntitle: microbial biomass nitrogen\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n method are required\nexamples:\n- value: 0.05 ug N/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 12\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_n\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThis document provides guidance on how to migrate from one version of the NMDC Schema to another.
smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool
URI: nmdc:min_q_value
","text":""},{"location":"min_q_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"min_q_value/#properties","title":"Properties","text":"name: min_q_value\ndescription: smallest Q-Value associated with the peptide sequence as provided by\n MSGFPlus tool\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- OBI:0001442\nrank: 1000\nalias: min_q_value\ndomain_of:\n- PeptideQuantification\nrange: float\n\nInformation about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens
URI: MIXS:0000570
"},{"location":"mineral_nutr_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: mineral_nutr_regm\nannotations:\n expected_value:\n tag: expected_value\n value: mineral nutrient name;mineral nutrient amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the use of mineral supplements;\n should include the name of mineral nutrient, amount administered, treatment regimen\n including how many times the treatment was repeated, how long each treatment lasted,\n and the start and end time of the entire treatment; can include multiple mineral\n nutrient regimens\ntitle: mineral nutrient regimen\nexamples:\n- value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000570\nalias: mineral_nutr_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAny other measurement performed or parameter collected, that is not listed here
URI: MIXS:0000752
"},{"location":"misc_param/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: misc_param\nannotations:\n expected_value:\n tag: expected_value\n value: parameter name;measurement value\n occurrence:\n tag: occurrence\n value: m\ndescription: Any other measurement performed or parameter collected, that is not listed\n here\ntitle: miscellaneous parameter\nexamples:\n- value: Bicarbonate ion concentration;2075 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- miscellaneous parameter\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000752\nalias: misc_param\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe last date on which the database information was modified.
URI: nmdc:mod_date
"},{"location":"mod_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Biosample Biological source material which can be characterized by an experiment no"},{"location":"mod_date/#properties","title":"Properties","text":"name: mod_date\ndescription: The last date on which the database information was modified.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mod_date\ndomain_of:\n- Biosample\n- DataGeneration\nrange: string\n\nURI: nmdc:model
"},{"location":"model/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Instrument A material entity that is designed to perform a function in a scientific inve... no"},{"location":"model/#properties","title":"Properties","text":"name: model\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: model\ndomain_of:\n- Instrument\nrange: InstrumentModelEnum\n\nThe type of modification being done
URI: nmdc:modifier_substance
"},{"location":"modifier_substance/#properties","title":"Properties","text":"name: modifier_substance\ndescription: The type of modification being done\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: modifier_substance\nrange: string\n\nConcentration of n-alkanes; can include multiple n-alkanes
URI: MIXS:0000503
"},{"location":"n_alkanes/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: n_alkanes\nannotations:\n expected_value:\n tag: expected_value\n value: n-alkane name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of n-alkanes; can include multiple n-alkanes\ntitle: n-alkanes\nexamples:\n- value: n-hexadecane;100 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- n-alkanes\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000503\nalias: n_alkanes\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA human readable label for an entity
URI: nmdc:name
"},{"location":"name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Manifest A qualified collection of DataObjects that can be analyzed together in the sa... no OrthologyGroup A set of genes or gene products in which all members are orthologous no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no MaterialEntity no ProcessedSample no NamedThing a databased entity or concept/class no Configuration A set of parameters that define the actions of a process and is shared among ... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no GeneProduct A molecule encoded by a gene that has an evolved function no MetatranscriptomeAnnotation no EnvironmentalMaterialTerm no NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Study A study summarizes the overall goal of a research initiative and outlines the... yes CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no PersonValue An attribute value representing a person yes OntologyClass A representation of class defined in an external ontology no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no CalibrationInformation A calibration object that is associated with a process no LibraryPreparation no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no MetatranscriptomeAssembly no Protocol no Biosample Biological source material which can be characterized by an experiment no WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no DataObject An object that primarily consists of symbols that represent information yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no Instrument A material entity that is designed to perform a function in a scientific inve... no ProtocolExecution A PlannedProces that has PlannedProcess parts no Sample A sample is a material entity that can be characterized by an experiment no Site no MetaproteomicsAnalysis no PlannedProcess no"},{"location":"name/#properties","title":"Properties","text":"name: name\ndescription: A human readable label for an entity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: name\ndomain_of:\n- PersonValue\n- NamedThing\n- Protocol\nrange: string\n\nComma delimited ordered list of NCBI taxonomy names.
URI: nmdc:ncbi_lineage
"},{"location":"ncbi_lineage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"ncbi_lineage/#properties","title":"Properties","text":"name: ncbi_lineage\ndescription: Comma delimited ordered list of NCBI taxonomy names.\ncomments:\n- Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_lineage\ndomain_of:\n- EukEval\nrange: string\n\nDash-delimited ordered list of NCBI taxonomy identifiers (TaxId)
URI: nmdc:ncbi_lineage_tax_ids
"},{"location":"ncbi_lineage_tax_ids/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"ncbi_lineage_tax_ids/#properties","title":"Properties","text":"Range: String
Regex pattern: ^\\d+(-\\d+)*$
name: ncbi_lineage_tax_ids\ndescription: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)\ncomments:\n- Example 1-131567-2759-2611352-33682-191814-2603949\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_lineage_tax_ids\ndomain_of:\n- EukEval\nrange: string\npattern: ^\\d+(-\\d+)*$\n\nURI: nmdc:ncbi_project_name
"},{"location":"ncbi_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"ncbi_project_name/#properties","title":"Properties","text":"name: ncbi_project_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_project_name\ndomain_of:\n- NucleotideSequencing\nrange: string\n\nURI: nmdc:ncbi_taxonomy_name
"},{"location":"ncbi_taxonomy_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ncbi_taxonomy_name/#properties","title":"Properties","text":"name: ncbi_taxonomy_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_taxonomy_name\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:neon_biosample_identifiers
"},{"location":"neon_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: neon_biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- neon_identifiers\nalias: neon_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nidentifiers for entities according to NEON
URI: nmdc:neon_identifiers
"},{"location":"neon_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain neon_study_identifiers None Study neon_biosample_identifiers None Biosample"},{"location":"neon_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: neon_identifiers\ndescription: identifiers for entities according to NEON\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: neon_identifiers\nrange: string\n\nURI: nmdc:neon_study_identifiers
"},{"location":"neon_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: neon_study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- neon_identifiers\nalias: neon_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nConcentration of nitrate in the sample
URI: MIXS:0000425
"},{"location":"nitrate/#inheritance","title":"Inheritance","text":"name: nitrate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrate in the sample\ntitle: nitrate\nexamples:\n- value: 65 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000425\nalias: nitrate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of nitrate nitrogen in the sample
URI: nmdc:nitrate_nitrogen
"},{"location":"nitrate_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrate_nitrogen/#properties","title":"Properties","text":"name: nitrate_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrate nitrogen in the sample\ntitle: nitrate_nitrogen\ncomments:\n- often below some specified limit of detection\nexamples:\n- value: 0.29 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrate_nitrogen\n- NO3-N\nrank: 1000\nalias: nitrate_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrite in the sample
URI: MIXS:0000426
"},{"location":"nitrite/#inheritance","title":"Inheritance","text":"name: nitrite\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrite in the sample\ntitle: nitrite\nexamples:\n- value: 0.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000426\nalias: nitrite\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of nitrite nitrogen in the sample
URI: nmdc:nitrite_nitrogen
"},{"location":"nitrite_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrite_nitrogen/#properties","title":"Properties","text":"name: nitrite_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrite nitrogen in the sample\ntitle: nitrite_nitrogen\nexamples:\n- value: 1.2 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrite_nitrogen\n- NO2-N\nrank: 1000\nalias: nitrite_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrogen (total)
URI: MIXS:0000504
"},{"location":"nitro/#inheritance","title":"Inheritance","text":"name: nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrogen (total)\ntitle: nitrogen\nexamples:\n- value: 4.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000504\nalias: nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nAmount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;
URI: nmdc:non_microb_biomass
"},{"location":"non_microb_biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass/#properties","title":"Properties","text":"name: non_microb_biomass\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n e.g.insect, plant, total. Can include multiple measurements separated by ;\ntitle: non-microbial biomass\nexamples:\n- value: insect 0.23 ug; plant 1g\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000174\n- MIXS:0000650\nrank: 8\nstring_serialization: '{text};{float} {unit}'\nalias: non_microb_biomass\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nReference or method used in determining biomass
URI: nmdc:non_microb_biomass_method
"},{"location":"non_microb_biomass_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass_method/#properties","title":"Properties","text":"name: non_microb_biomass_method\ndescription: Reference or method used in determining biomass\ntitle: non-microbial biomass method\ncomments:\n- required if \"non-microbial biomass\" is provided\nexamples:\n- value: https://doi.org/10.1038/s41467-021-26181-3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 9\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: non_microb_biomass_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nInformation about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens
URI: MIXS:0000571
"},{"location":"non_min_nutr_regm/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: non_min_nutr_regm\nannotations:\n expected_value:\n tag: expected_value\n value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the exposure of plant to non-mineral\n nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n nutrient, amount administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple non-mineral nutrient regimens\ntitle: non-mineral nutrient regimen\nexamples:\n- value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- non-mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000571\nalias: non_min_nutr_regm\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\nURI: nmdc:notes
"},{"location":"notes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"notes/#properties","title":"Properties","text":"name: notes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: notes\ndomain_of:\n- Study\nrange: string\n\nA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids
URI: MIXS:0000038
"},{"location":"nucl_acid_amp/#inheritance","title":"Inheritance","text":"name: nucl_acid_amp\nannotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of\n specific nucleic acids\ntitle: nucleic acid amplification\nexamples:\n- value: https://phylogenomics.me/protocols/16s-pcr-protocol/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid amplification\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000038\nalias: nucl_acid_amp\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\nA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample
URI: MIXS:0000037
"},{"location":"nucl_acid_ext/#inheritance","title":"Inheritance","text":"name: nucl_acid_ext\nannotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n procedure (SOP), that describes the material separation to recover the nucleic acid\n fraction from a sample\ntitle: nucleic acid extraction\nexamples:\n- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid extraction\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000037\nalias: nucl_acid_ext\nrange: TextValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:nucleic_acid_sequence_source_field
"},{"location":"nucleic_acid_sequence_source_field/#inheritance","title":"Inheritance","text":"name: nucleic acid sequence source field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: nucleic_acid_sequence_source_field\ndomain_of:\n- Biosample\nrange: string\n\nNumber of 16s sequences detected, a subunit of prokaryotic ribosomes.
URI: nmdc:num_16s
"},{"location":"num_16s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_16s/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: num_16s\ndescription: Number of 16s sequences detected, a subunit of prokaryotic ribosomes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- NCIT:C105370\nrank: 1000\nalias: num_16s\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nNumber of 23 seqeuences detected, a subunit of ribosomes.
URI: nmdc:num_23s
"},{"location":"num_23s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_23s/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: num_23s\ndescription: Number of 23 seqeuences detected, a subunit of ribosomes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OMIT:0013245\nrank: 1000\nalias: num_23s\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nNumber of 5s seqeuences detected, a subunit of ribosomes.
URI: nmdc:num_5s
"},{"location":"num_5s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_5s/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: num_5s\ndescription: Number of 5s seqeuences detected, a subunit of ribosomes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OMIT:0013248\nrank: 1000\nalias: num_5s\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nThe sequence count number of input reads aligned to assembled contigs.
URI: nmdc:num_aligned_reads
"},{"location":"num_aligned_reads/#inheritance","title":"Inheritance","text":"name: num_aligned_reads\ndescription: The sequence count number of input reads aligned to assembled contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_aligned_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sequence count number of input reads for assembly.
URI: nmdc:num_input_reads
"},{"location":"num_input_reads/#inheritance","title":"Inheritance","text":"name: num_input_reads\ndescription: The sequence count number of input reads for assembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_input_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nNumber of transfer transfer RNAs.
URI: nmdc:num_t_rna
"},{"location":"num_t_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_t_rna/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: num_t_rna\ndescription: Number of transfer transfer RNAs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- NCIT:C816\nrank: 1000\nalias: num_t_rna\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nNumber of contigs
URI: nmdc:number_of_contig
"},{"location":"number_of_contig/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"number_of_contig/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: number_of_contig\ndescription: Number of contigs\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- GENEPIO:0000093\nrank: 1000\nalias: number_of_contig\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nThe number of pets residing in the sampled space
URI: MIXS:0000231
"},{"location":"number_pets/#inheritance","title":"Inheritance","text":"name: number_pets\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of pets residing in the sampled space\ntitle: number of pets\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of pets\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000231\nalias: number_pets\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of plant(s) in the sampling space
URI: MIXS:0000230
"},{"location":"number_plants/#inheritance","title":"Inheritance","text":"name: number_plants\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of plant(s) in the sampling space\ntitle: number of houseplants\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of houseplants\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000230\nalias: number_plants\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of individuals currently occupying in the sampling location
URI: MIXS:0000232
"},{"location":"number_resident/#inheritance","title":"Inheritance","text":"name: number_resident\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of individuals currently occupying in the sampling location\ntitle: number of residents\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of residents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000232\nalias: number_resident\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:object
"},{"location":"object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyRelation A relationship between two ontology classes as specified either directly in t... no"},{"location":"object/#properties","title":"Properties","text":"Range: OntologyClass
Required: True
name: object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: object\nowner: OntologyRelation\ndomain_of:\n- OntologyRelation\nrange: OntologyClass\nrequired: true\n\nApplies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types
URI: nmdc:object_set
"},{"location":"object_set/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain chemical_entity_set This property links a database object to the set of chemical entities within ... None ontology_class_set This property links a database object to the set of ontology classes within i... OntologyClass biosample_set This property links a database object to the set of samples within it Biosample Database study_set This property links a database object to the set of studies within it Study Database field_research_site_set FieldResearchSite Database collecting_biosamples_from_site_set CollectingBiosamplesFromSite Database data_object_set This property links a database object to the set of data objects within it DataObject Database genome_feature_set This property links a database object to the set of all features GenomeFeature Database functional_annotation_set This property links a database object to the set of all functional annotation... FunctionalAnnotation Database workflow_execution_set This property links a database object to the set of workflow executions WorkflowExecution Database data_generation_set This property links a database object to the set of data generations within i... DataGeneration Database processed_sample_set This property links a database object to the set of processed samples within ... ProcessedSample Database instrument_set This property links a database object to the set of instruments within it Instrument Database calibration_set This property links a database object to the set of calibrations within it CalibrationInformation Database configuration_set This property links a database object to the set of configurations within it Configuration Database manifest_set This property links a database object to the set of manifests within it Manifest Database protocol_execution_set This property links a database object to the set of protocol executions withi... ProtocolExecution Database storage_process_set This property links a database object to the set of storage processes within ... StorageProcess Database material_processing_set This property links a database object to the set of material processing withi... MaterialProcessing Database"},{"location":"object_set/#properties","title":"Properties","text":"Range: String
Multivalued: True
Mixin: True
name: object_set\ndescription: Applies to a property that links a database object to a set of objects.\n This is necessary in a json document to provide context for a list, and to allow\n for a single json object that combines multiple object types\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: object_set\nrange: string\nmultivalued: true\ninlined_as_list: true\n\nThe scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.
URI: nmdc:objective
"},{"location":"objective/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"objective/#properties","title":"Properties","text":"name: objective\ndescription: The scientific objectives associated with the entity. It SHOULD correspond\n to scientific norms for objectives field in a structured abstract.\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- SIO:000337\nrank: 1000\nalias: objective\ndomain_of:\n- Study\nrange: string\n\nAverage number of occupants at time of sampling per square footage
URI: MIXS:0000217
"},{"location":"occup_density_samp/#inheritance","title":"Inheritance","text":"name: occup_density_samp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Average number of occupants at time of sampling per square footage\ntitle: occupant density at sampling\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupant density at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000217\nalias: occup_density_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of documentation of occupancy
URI: MIXS:0000816
"},{"location":"occup_document/#inheritance","title":"Inheritance","text":"name: occup_document\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of documentation of occupancy\ntitle: occupancy documentation\nexamples:\n- value: estimate\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy documentation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000816\nalias: occup_document\ndomain_of:\n- Biosample\nrange: occup_document_enum\nmultivalued: false\n\nNumber of occupants present at time of sample within the given space
URI: MIXS:0000772
"},{"location":"occup_samp/#inheritance","title":"Inheritance","text":"name: occup_samp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Number of occupants present at time of sample within the given space\ntitle: occupancy at sampling\nexamples:\n- value: '10'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000772\nalias: occup_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:omics_processing_identifiers
"},{"location":"omics_processing_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: omics_processing_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: omics_processing_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThe type of omics data
URI: nmdc:omics_type
","text":""},{"location":"omics_type/#properties","title":"Properties","text":"name: omics_type\ndescription: The type of omics data\ndeprecated: 'True'\nexamples:\n- value: metatranscriptome\n- value: metagenome\nfrom_schema: https://w3id.org/nmdc/nmdc\ndeprecated_element_has_exact_replacement: analyte_category\nrank: 1000\nalias: omics_type\nrange: string\n\nThis property links a database object to the set of ontology classes within it.
URI: nmdc:ontology_class_set
"},{"location":"ontology_class_set/#inheritance","title":"Inheritance","text":"Range: OntologyClass
Multivalued: True
name: ontology_class_set\ndescription: This property links a database object to the set of ontology classes\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: ontology_class_set\nrange: OntologyClass\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe ORCID of a person.
URI: nmdc:orcid
"},{"location":"orcid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"orcid/#properties","title":"Properties","text":"name: orcid\ndescription: The ORCID of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: orcid\ndomain_of:\n- PersonValue\nrange: string\n\nThe solution(s) that moves through a chromatography column.
URI: nmdc:ordered_mobile_phases
"},{"location":"ordered_mobile_phases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no"},{"location":"ordered_mobile_phases/#properties","title":"Properties","text":"Range: MobilePhaseSegment
Multivalued: True
name: ordered_mobile_phases\ndescription: The solution(s) that moves through a chromatography column.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: ordered_mobile_phases\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: MobilePhaseSegment\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of organic carbon
URI: MIXS:0000508
"},{"location":"org_carb/#inheritance","title":"Inheritance","text":"name: org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic carbon\ntitle: organic carbon\nexamples:\n- value: 1.5 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000508\nalias: org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nIf qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)
URI: MIXS:0000099
"},{"location":"org_count_qpcr_info/#inheritance","title":"Inheritance","text":"name: org_count_qpcr_info\nannotations:\n expected_value:\n tag: expected_value\n value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles\n preferred_unit:\n tag: preferred_unit\n value: number of cells per gram (or ml or cm^2)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'If qpcr was used for the cell count, the target gene name, the primer\n sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n 30 cycles)'\ntitle: organism count qPCR information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count qPCR information\nrank: 1000\nis_a: core field\nstring_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles'\nslot_uri: MIXS:0000099\nalias: org_count_qpcr_info\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nConcentration of organic matter
URI: MIXS:0000204
"},{"location":"org_matter/#inheritance","title":"Inheritance","text":"name: org_matter\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic matter\ntitle: organic matter\nexamples:\n- value: 1.75 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000204\nalias: org_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of organic nitrogen
URI: MIXS:0000205
"},{"location":"org_nitro/#inheritance","title":"Inheritance","text":"name: org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic nitrogen\ntitle: organic nitrogen\nexamples:\n- value: 4 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000205\nalias: org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMethod used for obtaining organic nitrogen
URI: nmdc:org_nitro_method
"},{"location":"org_nitro_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_nitro_method/#properties","title":"Properties","text":"name: org_nitro_method\ndescription: Method used for obtaining organic nitrogen\ntitle: organic nitrogen method\ncomments:\n- required if \"org_nitro\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(85)90144-0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000338\n- MIXS:0000205\nrank: 14\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: org_nitro_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nConcentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.
URI: MIXS:0000665
"},{"location":"org_particles/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: org_particles\nannotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of particles such as faeces, hairs, food, vomit, paper\n fibers, plant material, humus, etc.\ntitle: organic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000665\nalias: org_particles\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTotal cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)
URI: MIXS:0000103
"},{"location":"organism_count/#inheritance","title":"Inheritance","text":"Range: QuantityValue
Multivalued: True
name: organism_count\nannotations:\n expected_value:\n tag: expected_value\n value: organism name;measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: number of cells per cubic meter, number of cells per milliliter, number\n of cells per cubic centimeter\n occurrence:\n tag: occurrence\n value: m\ndescription: 'Total cell count of any organism (or group of organisms) per gram, volume\n or area of sample, should include name of organism followed by count. The method\n that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided.\n (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\ntitle: organism count\nexamples:\n- value: total prokaryotes;3.5e7 cells per milliliter;qPCR\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000103\nalias: organism_count\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nOther treatments applied to your samples that are not applicable to the provided fields
URI: nmdc:other_treatment
"},{"location":"other_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"other_treatment/#properties","title":"Properties","text":"Range: String
Recommended: True
name: other_treatment\ndescription: Other treatments applied to your samples that are not applicable to the\n provided fields\ntitle: other treatments\nnotes:\n- Values entered here will be used to determine potential new slots.\ncomments:\n- This is an open text field to provide any treatments that cannot be captured in\n the provided slots.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000300\nrank: 15\nstring_serialization: '{text}'\nalias: other_treatment\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nAfter QC analysis nucleotide base count number.
URI: nmdc:output_base_count
"},{"location":"output_base_count/#inheritance","title":"Inheritance","text":"name: output_base_count\ndescription: After QC analysis nucleotide base count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_base_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nTODO
URI: nmdc:output_read_bases
"},{"location":"output_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_read_bases/#properties","title":"Properties","text":"name: output_read_bases\ndescription: TODO\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: output_read_bases\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nAfter QC analysis sequence count number.
URI: nmdc:output_read_count
"},{"location":"output_read_count/#inheritance","title":"Inheritance","text":"name: output_read_count\ndescription: After QC analysis sequence count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_read_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nDepth of the original oil water contact (OWC) zone (average) (m TVDSS)
URI: MIXS:0000405
"},{"location":"owc_tvdss/#inheritance","title":"Inheritance","text":"name: owc_tvdss\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\ntitle: oil water contact depth\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oil water contact depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000405\nalias: owc_tvdss\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nOxygenation status of sample
URI: MIXS:0000753
"},{"location":"oxy_stat_samp/#inheritance","title":"Inheritance","text":"name: oxy_stat_samp\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oxygenation status of sample\ntitle: oxygenation status of sample\nexamples:\n- value: aerobic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygenation status of sample\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000753\nalias: oxy_stat_samp\ndomain_of:\n- Biosample\nrange: oxy_stat_samp_enum\nmultivalued: false\n\nOxygen (gas) amount or concentration at the time of sampling
URI: MIXS:0000104
"},{"location":"oxygen/#inheritance","title":"Inheritance","text":"name: oxygen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oxygen (gas) amount or concentration at the time of sampling\ntitle: oxygen\nexamples:\n- value: 600 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000104\nalias: oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nLinks a resource to another resource that either logically or physically includes it.
URI: dcterms:isPartOf
"},{"location":"part_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes"},{"location":"part_of/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: part_of\ndescription: Links a resource to another resource that either logically or physically\n includes it.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- is part of\nrank: 1000\nslot_uri: dcterms:isPartOf\nalias: part_of\ndomain_of:\n- FieldResearchSite\n- Study\nrange: NamedThing\nmultivalued: true\n\nConcentration of particulate organic carbon
URI: MIXS:0000515
"},{"location":"part_org_carb/#inheritance","title":"Inheritance","text":"name: part_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of particulate organic carbon\ntitle: particulate organic carbon\nexamples:\n- value: 1.92 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000515\nalias: part_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of particulate organic nitrogen
URI: MIXS:0000719
"},{"location":"part_org_nitro/#inheritance","title":"Inheritance","text":"name: part_org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of particulate organic nitrogen\ntitle: particulate organic nitrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000719\nalias: part_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nParticles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values
URI: MIXS:0000206
"},{"location":"particle_class/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: particle_class\nannotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: m\ndescription: Particles are classified, based on their size, into six general categories:clay,\n silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded\n by the name of the particle type; can include multiple values\ntitle: particle classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particle classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000206\nalias: particle_class\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nDescription of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'
URI: MIXS:0000049
"},{"location":"pcr_cond/#inheritance","title":"Inheritance","text":"name: pcr_cond\nannotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\ndescription: Description of reaction conditions and components of PCR in the form\n of 'initial denaturation:94degC_1.5min; annealing=...'\ntitle: pcr conditions\nexamples:\n- value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr conditions\nrank: 1000\nis_a: sequencing field\nstring_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\nslot_uri: MIXS:0000049\nalias: pcr_cond\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:pcr_cycles
"},{"location":"pcr_cycles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"pcr_cycles/#properties","title":"Properties","text":"name: pcr_cycles\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0002475\nrank: 1000\nalias: pcr_cycles\ndomain_of:\n- LibraryPreparation\nrange: integer\n\nPCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters
URI: MIXS:0000046
"},{"location":"pcr_primers/#inheritance","title":"Inheritance","text":"name: pcr_primers\nannotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\ndescription: PCR primers that were used to amplify the sequence of the targeted gene,\n locus or subfragment. This field should contain all the primers used for a single\n PCR reaction if multiple forward or reverse primers are present in a single PCR\n reaction. The primer sequence should be reported in uppercase letters\ntitle: pcr primers\nexamples:\n- value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr primers\nrank: 1000\nis_a: sequencing field\nstring_serialization: FWD:{dna};REV:{dna}\nslot_uri: MIXS:0000046\nalias: pcr_primers\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:peptide_sequence
","text":""},{"location":"peptide_sequence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sequence/#properties","title":"Properties","text":"name: peptide_sequence\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence\ndomain_of:\n- PeptideQuantification\nrange: string\n\ncount of peptide sequences grouped to the best_protein
URI: nmdc:peptide_sequence_count
","text":""},{"location":"peptide_sequence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"peptide_sequence_count/#properties","title":"Properties","text":"name: peptide_sequence_count\ndescription: count of peptide sequences grouped to the best_protein\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\nsum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file
URI: nmdc:peptide_spectral_count
","text":""},{"location":"peptide_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_spectral_count/#properties","title":"Properties","text":"name: peptide_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the peptide sequence\n within a given LC-MS/MS data file\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_spectral_count\ndomain_of:\n- PeptideQuantification\nrange: integer\n\ncombined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool
URI: nmdc:peptide_sum_masic_abundance
","text":""},{"location":"peptide_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sum_masic_abundance/#properties","title":"Properties","text":"name: peptide_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n with the peptide sequence from a given LC-MS/MS data file using the MASIC tool\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sum_masic_abundance\ndomain_of:\n- PeptideQuantification\nrange: integer\n\nMeasure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))
URI: MIXS:0000404
"},{"location":"permeability/#inheritance","title":"Inheritance","text":"name: permeability\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: mD\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Measure of the ability of a hydrocarbon resource to allow fluids to\n pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\ntitle: permeability\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- permeability\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} - {integer} {unit}'\nslot_uri: MIXS:0000404\nalias: permeability\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nType of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types
URI: MIXS:0000754
"},{"location":"perturbation/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: perturbation\nannotations:\n expected_value:\n tag: expected_value\n value: perturbation type name;perturbation interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Type of perturbation, e.g. chemical administration, physical disturbance,\n etc., coupled with perturbation regimen including how many times the perturbation\n was repeated, how long each perturbation lasted, and the start and end time of the\n entire perturbation period; can include multiple perturbation types\ntitle: perturbation\nexamples:\n- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- perturbation\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000754\nalias: perturbation\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nInformation about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens
URI: MIXS:0000573
"},{"location":"pesticide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: pesticide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: pesticide name;pesticide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of insecticides; should include\n the name of pesticide, amount administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple pesticide regimens\ntitle: pesticide regimen\nexamples:\n- value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pesticide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000573\nalias: pesticide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of petroleum hydrocarbon
URI: MIXS:0000516
"},{"location":"petroleum_hydrocarb/#inheritance","title":"Inheritance","text":"name: petroleum_hydrocarb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of petroleum hydrocarbon\ntitle: petroleum hydrocarbon\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- petroleum hydrocarbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000516\nalias: petroleum_hydrocarb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nPh measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
URI: MIXS:0001001
"},{"location":"ph/#inheritance","title":"Inheritance","text":"name: ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ph measurement of the sample, or liquid portion of sample, or aqueous\n phase of the fluid\ntitle: pH\nexamples:\n- value: '7.2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001001\nalias: ph\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\nReference or method used in determining ph
URI: MIXS:0001106
"},{"location":"ph_meth/#inheritance","title":"Inheritance","text":"name: ph_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining ph\ntitle: pH method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001106\nalias: ph_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen
URI: MIXS:0001056
"},{"location":"ph_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: ph_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving exposure of plants to varying levels\n of ph of the growth media, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple regimen\ntitle: pH regimen\nexamples:\n- value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001056\nalias: ph_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of phaeopigments; can include multiple phaeopigments
URI: MIXS:0000180
"},{"location":"phaeopigments/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: phaeopigments\nannotations:\n expected_value:\n tag: expected_value\n value: phaeopigment name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of phaeopigments; can include multiple phaeopigments\ntitle: phaeopigments\nexamples:\n- value: 2.5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phaeopigments\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000180\nalias: phaeopigments\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.
URI: nmdc:phase
"},{"location":"phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"phase/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
Maximum Value: 2
name: phase\ndescription: The phase for a coding sequence entity. For example, phase of a CDS as\n represented in a GFF3 with a value of 0, 1 or 2.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:phase\nrank: 1000\nalias: phase\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 0\nmaximum_value: 2\n\nConcentration of phosphate
URI: MIXS:0000505
"},{"location":"phosphate/#inheritance","title":"Inheritance","text":"name: phosphate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of phosphate\ntitle: phosphate\nexamples:\n- value: 0.7 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000505\nalias: phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of phospholipid fatty acids; can include multiple values
URI: MIXS:0000181
"},{"location":"phosplipid_fatt_acid/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: phosplipid_fatt_acid\nannotations:\n expected_value:\n tag: expected_value\n value: phospholipid fatty acid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per gram, mole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of phospholipid fatty acids; can include multiple values\ntitle: phospholipid fatty acid\nexamples:\n- value: 2.98 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phospholipid fatty acid\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000181\nalias: phosplipid_fatt_acid\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nMeasurement of photon flux
URI: MIXS:0000725
"},{"location":"photon_flux/#inheritance","title":"Inheritance","text":"name: photon_flux\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: number of photons per second per unit area\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of photon flux\ntitle: photon flux\nexamples:\n- value: 3.926 micromole photons per second per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- photon flux\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000725\nalias: photon_flux\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSpecification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary
URI: MIXS:0001057
"},{"location":"plant_growth_med/#inheritance","title":"Inheritance","text":"name: plant_growth_med\nannotations:\n expected_value:\n tag: expected_value\n value: EO or enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specification of the media for growing the plants or tissue cultured\n samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro\n liquid culture medium. Recommended value is a specific value from EO:plant growth\n medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or\n other controlled vocabulary\ntitle: plant growth medium\nexamples:\n- value: hydroponic plant culture media [EO:0007067]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant growth medium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001057\nalias: plant_growth_med\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nSubstance produced by the plant, where the sample was obtained from
URI: MIXS:0001058
"},{"location":"plant_product/#inheritance","title":"Inheritance","text":"name: plant_product\nannotations:\n expected_value:\n tag: expected_value\n value: product name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Substance produced by the plant, where the sample was obtained from\ntitle: plant product\nexamples:\n- value: xylem sap [PO:0025539]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant product\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001058\nalias: plant_product\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.
URI: MIXS:0001059
"},{"location":"plant_sex/#inheritance","title":"Inheritance","text":"name: plant_sex\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate,\n monoecieous, hermaphrodite.\ntitle: plant sex\nexamples:\n- value: Hermaphroditic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001059\nalias: plant_sex\ndomain_of:\n- Biosample\nrange: plant_sex_enum\nmultivalued: false\n\nName of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.
URI: MIXS:0001060
"},{"location":"plant_struc/#inheritance","title":"Inheritance","text":"name: plant_struc\nannotations:\n expected_value:\n tag: expected_value\n value: PO\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of plant structure the sample was obtained from; for Plant Ontology\n (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex\n of it can be recorded here.\ntitle: plant structure\nexamples:\n- value: epidermis [PO:0005679]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant structure\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0001060\nalias: plant_struc\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nthe polarity of which ions are generated and detected
URI: nmdc:polarity_mode
"},{"location":"polarity_mode/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"polarity_mode/#properties","title":"Properties","text":"name: polarity_mode\ndescription: the polarity of which ions are generated and detected\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: polarity_mode\ndomain_of:\n- MassSpectrometryConfiguration\nrange: PolarityModeEnum\n\nPollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant
URI: MIXS:0000107
"},{"location":"pollutants/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: pollutants\nannotations:\n expected_value:\n tag: expected_value\n value: pollutant name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter, microgram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Pollutant types and, amount or concentrations measured at the time of\n sampling; can report multiple pollutants by entering numeric values preceded by\n name of pollutant\ntitle: pollutants\nexamples:\n- value: lead;0.15 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pollutants\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000107\nalias: pollutants\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nIndicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given
URI: MIXS:0000325
"},{"location":"pool_dna_extracts/#inheritance","title":"Inheritance","text":"name: pool_dna_extracts\nannotations:\n expected_value:\n tag: expected_value\n value: pooling status;number of pooled extracts\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Indicate whether multiple DNA extractions were mixed. If the answer yes,\n the number of extracts that were pooled should be given\ntitle: pooling of DNA extracts (if done)\nexamples:\n- value: yes;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pooling of DNA extracts (if done)\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{integer}'\nslot_uri: MIXS:0000325\nalias: pool_dna_extracts\nrange: TextValue\nmultivalued: false\n\nPorosity of deposited sediment is volume of voids divided by the total volume of sample
URI: MIXS:0000211
"},{"location":"porosity/#inheritance","title":"Inheritance","text":"name: porosity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value or range\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Porosity of deposited sediment is volume of voids divided by the total\n volume of sample\ntitle: porosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- porosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000211\nalias: porosity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of potassium in the sample
URI: MIXS:0000430
"},{"location":"potassium/#inheritance","title":"Inheritance","text":"name: potassium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of potassium in the sample\ntitle: potassium\nexamples:\n- value: 463 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- potassium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000430\nalias: potassium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTemperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)
URI: MIXS:0000127
"},{"location":"pour_point/#inheritance","title":"Inheritance","text":"name: pour_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Temperature at which a liquid becomes semi solid and loses its flow\n characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a\n high paraffin content, typically found in crude deriving from a larger proportion\n of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\ntitle: pour point\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pour point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000127\nalias: pour_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe process of pre-treatment removes materials that can be easily collected from the raw wastewater
URI: MIXS:0000348
"},{"location":"pre_treatment/#inheritance","title":"Inheritance","text":"name: pre_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: pre-treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process of pre-treatment removes materials that can be easily collected\n from the raw wastewater\ntitle: pre-treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pre-treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000348\nalias: pre_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:predicate
"},{"location":"predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyRelation A relationship between two ontology classes as specified either directly in t... no"},{"location":"predicate/#properties","title":"Properties","text":"Range: OntologyClass
Required: True
name: predicate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: predicate\nowner: OntologyRelation\ndomain_of:\n- OntologyRelation\nrange: OntologyClass\nrequired: true\n\nThe type and number of animals or insects present in the sampling space.
URI: MIXS:0000819
"},{"location":"pres_animal_insect/#inheritance","title":"Inheritance","text":"Range: String
Regex pattern: ^(cat|dog|rodent|snake|other);\\d+$
name: pres_animal_insect\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration;count\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type and number of animals or insects present in the sampling space.\ntitle: presence of pets, animals, or insects\nexamples:\n- value: cat;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- presence of pets, animals, or insects\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000819\nalias: pres_animal_insect\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\npattern: ^(cat|dog|rodent|snake|other);\\d+$\n\nPressure to which the sample is subject to, in atmospheres
URI: MIXS:0000412
"},{"location":"pressure/#inheritance","title":"Inheritance","text":"name: pressure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: atmosphere\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Pressure to which the sample is subject to, in atmospheres\ntitle: pressure\nexamples:\n- value: 50 atmosphere\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000412\nalias: pressure\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining previous land use and dates
URI: MIXS:0000316
"},{"location":"prev_land_use_meth/#inheritance","title":"Inheritance","text":"name: prev_land_use_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining previous land use and dates\ntitle: history/previous land use method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000316\nalias: prev_land_use_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nPrevious land use and dates
URI: MIXS:0000315
"},{"location":"previous_land_use/#inheritance","title":"Inheritance","text":"name: previous_land_use\nannotations:\n expected_value:\n tag: expected_value\n value: land use name;date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Previous land use and dates\ntitle: history/previous land use\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{timestamp}'\nslot_uri: MIXS:0000315\nalias: previous_land_use\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMeasurement of primary production, generally measured as isotope uptake
URI: MIXS:0000728
"},{"location":"primary_prod/#inheritance","title":"Inheritance","text":"name: primary_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, gram per square meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of primary production, generally measured as isotope uptake\ntitle: primary production\nexamples:\n- value: 100 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000728\nalias: primary_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed
URI: MIXS:0000349
"},{"location":"primary_treatment/#inheritance","title":"Inheritance","text":"name: primary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: primary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process to produce both a generally homogeneous liquid capable of\n being treated biologically and a sludge that can be separately treated or processed\ntitle: primary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000349\nalias: primary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nPrincipal Investigator who led the study and/or generated the dataset.
URI: nmdc:principal_investigator
"},{"location":"principal_investigator/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"principal_investigator/#properties","title":"Properties","text":"name: principal_investigator\ndescription: Principal Investigator who led the study and/or generated the dataset.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- PI\nrank: 1000\nalias: principal_investigator\ndomain_of:\n- Study\n- DataGeneration\nrange: PersonValue\n\nThis property links a database object to the set of processed samples within it.
URI: nmdc:processed_sample_set
"},{"location":"processed_sample_set/#inheritance","title":"Inheritance","text":"Range: ProcessedSample
Multivalued: True
name: processed_sample_set\ndescription: This property links a database object to the set of processed samples\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: processed_sample_set\ndomain_of:\n- Database\nrange: ProcessedSample\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe organization that processed the sample.
URI: nmdc:processing_institution
"},{"location":"processing_institution/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAnnotation no NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no LibraryPreparation no StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ProtocolExecution A PlannedProces that has PlannedProcess parts no MetaproteomicsAnalysis no PlannedProcess no"},{"location":"processing_institution/#properties","title":"Properties","text":"name: processing_institution\ndescription: The organization that processed the sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: processing_institution\ndomain_of:\n- PlannedProcess\nrange: ProcessingInstitutionEnum\n\nOil and/or gas production rates per well (e.g. 524 m3 / day)
URI: MIXS:0000452
"},{"location":"prod_rate/#inheritance","title":"Inheritance","text":"name: prod_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oil and/or gas production rates per well (e.g. 524 m3 / day)\ntitle: production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000452\nalias: prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDate of field's first production
URI: MIXS:0001008
"},{"location":"prod_start_date/#inheritance","title":"Inheritance","text":"name: prod_start_date\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Date of field's first production\ntitle: production start date\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001008\nalias: prod_start_date\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nA url that points to an image of a person.
URI: nmdc:profile_image_url
"},{"location":"profile_image_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person no"},{"location":"profile_image_url/#properties","title":"Properties","text":"name: profile_image_url\ndescription: A url that points to an image of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: profile_image_url\ndomain_of:\n- PersonValue\nrange: string\n\nCross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas
URI: MIXS:0001084
"},{"location":"profile_position/#inheritance","title":"Inheritance","text":"name: profile_position\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Cross-sectional position in the hillslope where sample was collected.sample\n area position in relation to surrounding areas\ntitle: profile position\nexamples:\n- value: summit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- profile position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001084\nalias: profile_position\ndomain_of:\n- Biosample\nrange: profile_position_enum\nmultivalued: false\n\nProposal IDs or names associated with dataset
URI: nmdc:project_id
"},{"location":"project_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"project_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: project_id\ndescription: Proposal IDs or names associated with dataset\ntitle: project ID\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: project_id\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nURI: nmdc:proport_woa_temperature
"},{"location":"proport_woa_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proport_woa_temperature/#properties","title":"Properties","text":"name: proport_woa_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: proport_woa_temperature\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:proposal_dna
"},{"location":"proposal_dna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_dna/#properties","title":"Properties","text":"Range: String
Recommended: True
name: proposal_dna\ntitle: DNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_dna\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:proposal_rna
"},{"location":"proposal_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_rna/#properties","title":"Properties","text":"Range: String
Recommended: True
name: proposal_rna\ntitle: RNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nsum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file
URI: nmdc:protein_spectral_count
","text":""},{"location":"protein_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_spectral_count/#properties","title":"Properties","text":"name: protein_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the best protein within\n a given LC-MS/MS data file\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_spectral_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\ncombined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool
URI: nmdc:protein_sum_masic_abundance
","text":""},{"location":"protein_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_sum_masic_abundance/#properties","title":"Properties","text":"name: protein_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n with the best protein from a given LC-MS/MS data file using the MASIC tool\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_sum_masic_abundance\ndomain_of:\n- ProteinQuantification\nrange: integer\n\nURI: nmdc:protocol_execution_category
"},{"location":"protocol_execution_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProtocolExecution A PlannedProces that has PlannedProcess parts no"},{"location":"protocol_execution_category/#properties","title":"Properties","text":"Range: ProtocolCategoryEnum
Required: True
name: protocol_execution_category\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_execution_category\ndomain_of:\n- ProtocolExecution\nrange: ProtocolCategoryEnum\nrequired: true\n\nThis property links a database object to the set of protocol executions within it.
URI: nmdc:protocol_execution_set
"},{"location":"protocol_execution_set/#inheritance","title":"Inheritance","text":"Range: ProtocolExecution
Multivalued: True
name: protocol_execution_set\ndescription: This property links a database object to the set of protocol executions\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: protocol_execution_set\ndomain_of:\n- Database\nrange: ProtocolExecution\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:protocol_link
"},{"location":"protocol_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAnnotation no NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no Study A study summarizes the overall goal of a research initiative and outlines the... yes CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no LibraryPreparation no StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ProtocolExecution A PlannedProces that has PlannedProcess parts no MetaproteomicsAnalysis no PlannedProcess no"},{"location":"protocol_link/#properties","title":"Properties","text":"name: protocol_link\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_link\ndomain_of:\n- PlannedProcess\n- Study\nrange: Protocol\n\nSlot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).
URI: nmdc:qc_comment
"},{"location":"qc_comment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAnnotation no NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no LibraryPreparation no StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ProtocolExecution A PlannedProces that has PlannedProcess parts no MetaproteomicsAnalysis no PlannedProcess no"},{"location":"qc_comment/#properties","title":"Properties","text":"name: qc_comment\ndescription: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed. (ie\n Failed at call-stage due to a malformed fastq file).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_comment\ndomain_of:\n- PlannedProcess\nrange: string\n\nProvides a summary about what caused a lab or workflow process to fail
URI: nmdc:qc_failure_what
"},{"location":"qc_failure_what/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FailureCategorization no"},{"location":"qc_failure_what/#properties","title":"Properties","text":"name: qc_failure_what\ndescription: Provides a summary about what caused a lab or workflow process to fail\ncomments:\n- For example, low read count from a sequencer, malformed fastq files, etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_failure_what\ndomain_of:\n- FailureCategorization\nrange: FailureWhatEnum\n\nDescribes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results.
URI: nmdc:qc_failure_where
"},{"location":"qc_failure_where/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FailureCategorization no"},{"location":"qc_failure_where/#properties","title":"Properties","text":"name: qc_failure_where\ndescription: Describes the nmdc schema class that corresonds to where the failure\n occurred. Most commonly this would be the same as Class that generated the results.\ncomments:\n- If the assembly size was too small to proceed to annotation failure_where would\n be MetagenomeAssembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_failure_where\ndomain_of:\n- FailureCategorization\nrange: FailureWhereEnum\n\nStores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)
URI: nmdc:qc_status
"},{"location":"qc_status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAnnotation no NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no LibraryPreparation no StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ProtocolExecution A PlannedProces that has PlannedProcess parts no MetaproteomicsAnalysis no PlannedProcess no"},{"location":"qc_status/#properties","title":"Properties","text":"name: qc_status\ndescription: Stores information about the result of a process (ie the process of sequencing\n a library may have for qc_status of 'fail' if not enough data was generated)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_status\ndomain_of:\n- PlannedProcess\nrange: StatusEnum\n\nThe quadrant position of the sampling room within the building
URI: MIXS:0000820
"},{"location":"quad_pos/#inheritance","title":"Inheritance","text":"name: quad_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The quadrant position of the sampling room within the building\ntitle: quadrant position\nexamples:\n- value: West side\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- quadrant position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000820\nalias: quad_pos\ndomain_of:\n- Biosample\nrange: quad_pos_enum\nmultivalued: false\n\nInformation about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens
URI: MIXS:0000575
"},{"location":"radiation_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: radiation_regm\nannotations:\n expected_value:\n tag: expected_value\n value: radiation type name;radiation amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: rad, gray\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving exposure of plant or a plant part\n to a particular radiation regimen; should include the radiation type, amount or\n intensity administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple radiation regimens\ntitle: radiation regimen\nexamples:\n- value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- radiation regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000575\nalias: radiation_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nInformation about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000576
"},{"location":"rainfall_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: rainfall_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to a given amount of\n rainfall, treatment regimen including how many times the treatment was repeated,\n how long each treatment lasted, and the start and end time of the entire treatment;\n can include multiple regimens\ntitle: rainfall regimen\nexamples:\n- value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rainfall regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000576\nalias: rainfall_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAnaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage
URI: MIXS:0000350
"},{"location":"reactor_type/#inheritance","title":"Inheritance","text":"name: reactor_type\nannotations:\n expected_value:\n tag: expected_value\n value: reactor type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Anaerobic digesters can be designed and engineered to operate using a\n number of different process configurations, as batch or continuous, mesophilic,\n high solid or low solid, and single stage or multistage\ntitle: reactor type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reactor type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000350\nalias: reactor_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:read_qc_analysis_statistic
"},{"location":"read_qc_analysis_statistic/#inheritance","title":"Inheritance","text":"name: read_qc_analysis_statistic\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: read_qc_analysis_statistic\nrange: string\n\nRedox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
URI: MIXS:0000182
"},{"location":"redox_potential/#inheritance","title":"Inheritance","text":"name: redox_potential\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millivolt\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Redox potential, measured relative to a hydrogen cell, indicating oxidation\n or reduction potential\ntitle: redox potential\nexamples:\n- value: 300 millivolt\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- redox potential\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000182\nalias: redox_potential\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nPartial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air
URI: MIXS:0000121
"},{"location":"rel_air_humidity/#inheritance","title":"Inheritance","text":"name: rel_air_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Partial vapor and air pressure, density of the vapor and air, or by the\n actual mass of the vapor and air\ntitle: relative air humidity\nexamples:\n- value: 80%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000121\nalias: rel_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe recorded outside relative humidity value at the time of sampling
URI: MIXS:0000188
"},{"location":"rel_humidity_out/#inheritance","title":"Inheritance","text":"name: rel_humidity_out\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded outside relative humidity value at the time of sampling\ntitle: outside relative humidity\nexamples:\n- value: 12 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- outside relative humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000188\nalias: rel_humidity_out\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe sampling location within the train car
URI: MIXS:0000821
"},{"location":"rel_samp_loc/#inheritance","title":"Inheritance","text":"name: rel_samp_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The sampling location within the train car\ntitle: relative sampling location\nexamples:\n- value: center of car\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative sampling location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000821\nalias: rel_samp_loc\ndomain_of:\n- Biosample\nrange: rel_samp_loc_enum\nmultivalued: false\n\nIdentifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation.
URI: nmdc:related_identifiers
"},{"location":"related_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"related_identifiers/#properties","title":"Properties","text":"name: related_identifiers\ndescription: Identifiers assigned to a thing that is similar to that which is represented\n in NMDC. Related identifier are not an identical match and may have some variation.\ntitle: Related Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: related_identifiers\ndomain_of:\n- Study\nrange: string\n\nURI: nmdc:relations
"},{"location":"relations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EnvironmentalMaterialTerm no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no OrthologyGroup A set of genes or gene products in which all members are orthologous no OntologyClass A representation of class defined in an external ontology no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"relations/#properties","title":"Properties","text":"Range: OntologyRelation
Multivalued: True
name: relations\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: relations\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: OntologyRelation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nIf sending biological replicates, indicate the rep number here.
URI: nmdc:replicate_number
"},{"location":"replicate_number/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"replicate_number/#properties","title":"Properties","text":"Range: String
Recommended: True
name: replicate_number\ndescription: If sending biological replicates, indicate the rep number here.\ntitle: replicate number\ncomments:\n- This will guide staff in ensuring your samples are blocked & randomized correctly\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{integer}'\nalias: replicate_number\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nName of the reservoir (e.g. Carapebus)
URI: MIXS:0000303
"},{"location":"reservoir/#inheritance","title":"Inheritance","text":"name: reservoir\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the reservoir (e.g. Carapebus)\ntitle: reservoir name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reservoir name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000303\nalias: reservoir\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000134
"},{"location":"resins_pc/#inheritance","title":"Inheritance","text":"name: resins_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: resins wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- resins wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000134\nalias: resins_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe relative resolution at which spectra were collected.
URI: nmdc:resolution_categories
"},{"location":"resolution_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"resolution_categories/#properties","title":"Properties","text":"Range: ResolutionCategoryEnum
Multivalued: True
name: resolution_categories\ndescription: The relative resolution at which spectra were collected.\nexamples:\n- value: '[''high'', ''low'']'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: resolution_categories\ndomain_of:\n- MassSpectrometryConfiguration\nrange: ResolutionCategoryEnum\nmultivalued: true\n\n260/280 measurement of RNA sample purity
URI: nmdc:rna_absorb1
"},{"location":"rna_absorb1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_absorb1/#properties","title":"Properties","text":"Range: Float
Recommended: True
name: rna_absorb1\ndescription: 260/280 measurement of RNA sample purity\ntitle: RNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nstring_serialization: '{float}'\nalias: rna_absorb1\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\n260/230 measurement of RNA sample purity
URI: nmdc:rna_absorb2
"},{"location":"rna_absorb2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_absorb2/#properties","title":"Properties","text":"Range: Float
Recommended: True
name: rna_absorb2\ndescription: 260/230 measurement of RNA sample purity\ntitle: RNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nstring_serialization: '{float}'\nalias: rna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\nProvide information on the site your RNA sample was collected from
URI: nmdc:rna_collect_site
"},{"location":"rna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_collect_site/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_collect_site\ndescription: Provide information on the site your RNA sample was collected from\ntitle: RNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: rna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_concentration
"},{"location":"rna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_concentration/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: rna_concentration\ntitle: RNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nstring_serialization: '{float}'\nalias: rna_concentration\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nTube or plate (96-well)
URI: nmdc:rna_cont_type
"},{"location":"rna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_type/#properties","title":"Properties","text":"Range: JgiContTypeEnum
Recommended: True
name: rna_cont_type\ndescription: Tube or plate (96-well)\ntitle: RNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: rna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: JgiContTypeEnum\nrecommended: true\n\nURI: nmdc:rna_cont_well
"},{"location":"rna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_well/#properties","title":"Properties","text":"Range: String
Recommended: True
Regex pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
name: rna_cont_well\ntitle: RNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: rna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\npattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n\nURI: nmdc:rna_container_id
"},{"location":"rna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_container_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_container_id\ntitle: RNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: rna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nDescribe the method/protocol/kit used to extract DNA/RNA.
URI: nmdc:rna_isolate_meth
"},{"location":"rna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_isolate_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: RNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Sample Isolation Method\nrank: 16\nstring_serialization: '{text}'\nalias: rna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nList any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.
URI: nmdc:rna_organisms
"},{"location":"rna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_organisms/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\ntitle: RNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: rna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_project_contact
"},{"location":"rna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_project_contact/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_project_contact\ntitle: RNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: rna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_samp_id
"},{"location":"rna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_samp_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_samp_id\ntitle: RNA sample ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: rna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nSolution in which the RNA sample has been suspended
URI: nmdc:rna_sample_format
"},{"location":"rna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_format/#properties","title":"Properties","text":"Range: RNASampleFormatEnum
Recommended: True
name: rna_sample_format\ndescription: Solution in which the RNA sample has been suspended\ntitle: RNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: rna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: RNASampleFormatEnum\nrecommended: true\n\nGive the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
URI: nmdc:rna_sample_name
"},{"location":"rna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_name/#properties","title":"Properties","text":"Range: String
Recommended: True
Minimum Value: 0
Maximum Value: 2000
name: rna_sample_name\ndescription: Give the RNA sample a name that is meaningful to you. Sample names must\n be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: RNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: rna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\nURI: nmdc:rna_seq_project
"},{"location":"rna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project\ntitle: RNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Seq Project ID\nrank: 1\nstring_serialization: '{text}'\nalias: rna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_seq_project_name
"},{"location":"rna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project_name\ntitle: RNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: JGI Pond metatranscriptomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: rna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_seq_project_pi
"},{"location":"rna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_pi/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project_pi\ntitle: RNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: rna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_volume
"},{"location":"rna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_volume/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: rna_volume\ntitle: RNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n accepts values < 25, but JGI may refuse to process them unless permission has been\n granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: rna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nThe rate at which outside air replaces indoor air in a given space
URI: MIXS:0000169
"},{"location":"room_air_exch_rate/#inheritance","title":"Inheritance","text":"name: room_air_exch_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The rate at which outside air replaces indoor air in a given space\ntitle: room air exchange rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room air exchange rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000169\nalias: room_air_exch_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure
URI: MIXS:0000233
"},{"location":"room_architec_elem/#inheritance","title":"Inheritance","text":"name: room_architec_elem\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The unique details and component parts that, together, form the architecture\n of a distinguisahable space within a built structure\ntitle: room architectural elements\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room architectural elements\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000233\nalias: room_architec_elem\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe condition of the room at the time of sampling
URI: MIXS:0000822
"},{"location":"room_condt/#inheritance","title":"Inheritance","text":"name: room_condt\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The condition of the room at the time of sampling\ntitle: room condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000822\nalias: room_condt\ndomain_of:\n- Biosample\nrange: room_condt_enum\nmultivalued: false\n\nList of rooms connected to the sampling room by a doorway
URI: MIXS:0000826
"},{"location":"room_connected/#inheritance","title":"Inheritance","text":"name: room_connected\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of rooms connected to the sampling room by a doorway\ntitle: rooms connected by a doorway\nexamples:\n- value: office\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms connected by a doorway\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000826\nalias: room_connected\ndomain_of:\n- Biosample\nrange: room_connected_enum\nmultivalued: false\n\nThe total count of rooms in the built structure including all room types
URI: MIXS:0000234
"},{"location":"room_count/#inheritance","title":"Inheritance","text":"name: room_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total count of rooms in the built structure including all room types\ntitle: room count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000234\nalias: room_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe length, width and height of sampling room
URI: MIXS:0000192
"},{"location":"room_dim/#inheritance","title":"Inheritance","text":"name: room_dim\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The length, width and height of sampling room\ntitle: room dimensions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room dimensions\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\nslot_uri: MIXS:0000192\nalias: room_dim\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDistance between doors (meters) in the hallway between the sampling room and adjacent rooms
URI: MIXS:0000193
"},{"location":"room_door_dist/#inheritance","title":"Inheritance","text":"name: room_door_dist\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Distance between doors (meters) in the hallway between the sampling room\n and adjacent rooms\ntitle: room door distance\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room door distance\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000193\nalias: room_door_dist\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of room(s) (room number, room name) sharing a door with the sampling room
URI: MIXS:0000242
"},{"location":"room_door_share/#inheritance","title":"Inheritance","text":"name: room_door_share\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) sharing a door with the sampling\n room\ntitle: rooms that share a door with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a door with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000242\nalias: room_door_share\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of room(s) (room number, room name) located in the same hallway as sampling room
URI: MIXS:0000238
"},{"location":"room_hallway/#inheritance","title":"Inheritance","text":"name: room_hallway\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) located in the same hallway\n as sampling room\ntitle: rooms that are on the same hallway\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that are on the same hallway\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000238\nalias: room_hallway\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe position of the room within the building
URI: MIXS:0000823
"},{"location":"room_loc/#inheritance","title":"Inheritance","text":"name: room_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The position of the room within the building\ntitle: room location in building\nexamples:\n- value: interior room\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room location in building\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000823\nalias: room_loc\ndomain_of:\n- Biosample\nrange: room_loc_enum\nmultivalued: false\n\nThe history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed
URI: MIXS:0000235
"},{"location":"room_moist_dam_hist/#inheritance","title":"Inheritance","text":"name: room_moist_dam_hist\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The history of moisture damage or mold in the past 12 months. Number\n of events of moisture damage or mold observed\ntitle: room moisture damage or mold history\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room moisture damage or mold history\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000235\nalias: room_moist_dam_hist\ndomain_of:\n- Biosample\nrange: integer\nmultivalued: false\n\nThe net floor area of sampling room. Net area excludes wall thicknesses
URI: MIXS:0000194
"},{"location":"room_net_area/#inheritance","title":"Inheritance","text":"name: room_net_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square feet, square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The net floor area of sampling room. Net area excludes wall thicknesses\ntitle: room net area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room net area\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000194\nalias: room_net_area\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nCount of room occupancy at time of sampling
URI: MIXS:0000236
"},{"location":"room_occup/#inheritance","title":"Inheritance","text":"name: room_occup\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Count of room occupancy at time of sampling\ntitle: room occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000236\nalias: room_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe horizontal sampling position in the room relative to architectural elements
URI: MIXS:0000824
"},{"location":"room_samp_pos/#inheritance","title":"Inheritance","text":"name: room_samp_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The horizontal sampling position in the room relative to architectural\n elements\ntitle: room sampling position\nexamples:\n- value: south corner\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room sampling position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000824\nalias: room_samp_pos\ndomain_of:\n- Biosample\nrange: room_samp_pos_enum\nmultivalued: false\n\nThe main purpose or activity of the sampling room. A room is any distinguishable space within a structure
URI: MIXS:0000825
"},{"location":"room_type/#inheritance","title":"Inheritance","text":"name: room_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The main purpose or activity of the sampling room. A room is any distinguishable\n space within a structure\ntitle: room type\nexamples:\n- value: bathroom\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000825\nalias: room_type\ndomain_of:\n- Biosample\nrange: room_type_enum\nmultivalued: false\n\nVolume of sampling room
URI: MIXS:0000195
"},{"location":"room_vol/#inheritance","title":"Inheritance","text":"name: room_vol\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic feet, cubic meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Volume of sampling room\ntitle: room volume\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room volume\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000195\nalias: room_vol\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of room(s) (room number, room name) sharing a wall with the sampling room
URI: MIXS:0000243
"},{"location":"room_wall_share/#inheritance","title":"Inheritance","text":"name: room_wall_share\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) sharing a wall with the sampling\n room\ntitle: rooms that share a wall with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a wall with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000243\nalias: room_wall_share\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nNumber of windows in the room
URI: MIXS:0000237
"},{"location":"room_window_count/#inheritance","title":"Inheritance","text":"name: room_window_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Number of windows in the room\ntitle: room window count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room window count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000237\nalias: room_window_count\ndomain_of:\n- Biosample\nrange: integer\nmultivalued: false\n\nRelevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.
URI: MIXS:0001061
"},{"location":"root_cond/#inheritance","title":"Inheritance","text":"name: root_cond\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Relevant rooting conditions such as field plot size, sowing density,\n container dimensions, number of plants per container.\ntitle: rooting conditions\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001061\nalias: root_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSource of organic carbon in the culture rooting medium; e.g. sucrose.
URI: MIXS:0000577
"},{"location":"root_med_carbon/#inheritance","title":"Inheritance","text":"name: root_med_carbon\nannotations:\n expected_value:\n tag: expected_value\n value: carbon source name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Source of organic carbon in the culture rooting medium; e.g. sucrose.\ntitle: rooting medium carbon\nexamples:\n- value: sucrose\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium carbon\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000577\nalias: root_med_carbon\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMeasurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).
URI: MIXS:0000578
"},{"location":"root_med_macronutr/#inheritance","title":"Inheritance","text":"name: root_med_macronutr\nannotations:\n expected_value:\n tag: expected_value\n value: macronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of the culture rooting medium macronutrients (N,P, K, Ca,\n Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\ntitle: rooting medium macronutrients\nexamples:\n- value: KH2PO4;170\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium macronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000578\nalias: root_med_macronutr\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMeasurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).
URI: MIXS:0000579
"},{"location":"root_med_micronutr/#inheritance","title":"Inheritance","text":"name: root_med_micronutr\nannotations:\n expected_value:\n tag: expected_value\n value: micronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn,\n B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\ntitle: rooting medium micronutrients\nexamples:\n- value: H3BO3;6.2\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium micronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000579\nalias: root_med_micronutr\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\npH measurement of the culture rooting medium; e.g. 5.5.
URI: MIXS:0001062
"},{"location":"root_med_ph/#inheritance","title":"Inheritance","text":"name: root_med_ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: pH measurement of the culture rooting medium; e.g. 5.5.\ntitle: rooting medium pH\nexamples:\n- value: '7.5'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001062\nalias: root_med_ph\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nGrowth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.
URI: MIXS:0000581
"},{"location":"root_med_regl/#inheritance","title":"Inheritance","text":"name: root_med_regl\nannotations:\n expected_value:\n tag: expected_value\n value: regulator name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Growth regulators in the culture rooting medium such as cytokinins, auxins,\n gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\ntitle: rooting medium regulators\nexamples:\n- value: abscisic acid;0.75 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium regulators\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000581\nalias: root_med_regl\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSpecification of the solidifying agent in the culture rooting medium; e.g. agar.
URI: MIXS:0001063
"},{"location":"root_med_solid/#inheritance","title":"Inheritance","text":"name: root_med_solid\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specification of the solidifying agent in the culture rooting medium;\n e.g. agar.\ntitle: rooting medium solidifier\nexamples:\n- value: agar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium solidifier\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001063\nalias: root_med_solid\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nOrganic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5\u00ac\u2020mg/L).
URI: MIXS:0000580
"},{"location":"root_med_suppl/#inheritance","title":"Inheritance","text":"name: root_med_suppl\nannotations:\n expected_value:\n tag: expected_value\n value: supplement name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Organic supplements of the culture rooting medium, such as vitamins,\n amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n (0.5\u00ac\u2020mg/L).\ntitle: rooting medium organic supplements\nexamples:\n- value: nicotinic acid;0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium organic supplements\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000580\nalias: root_med_suppl\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.
URI: MIXS:0000183
"},{"location":"salinity/#inheritance","title":"Inheritance","text":"name: salinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: practical salinity unit, percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total concentration of all dissolved salts in a liquid or solid sample.\n While salinity can be measured by a complete chemical analysis, this method is difficult\n and time consuming. More often, it is instead derived from the conductivity measurement.\n This is known as practical salinity. These derivations compare the specific conductance\n of the sample to a salinity standard such as seawater.\ntitle: salinity\nexamples:\n- value: 25 practical salinity unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000183\nalias: salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCategorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline
URI: nmdc:salinity_category
"},{"location":"salinity_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salinity_category/#properties","title":"Properties","text":"name: salinity_category\ndescription: 'Categorical description of the sample''s salinity. Examples: halophile,\n halotolerant, hypersaline, huryhaline'\nnotes:\n- maps to gold:salinity\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-metadata/pull/297\nrank: 1000\nalias: salinity_category\ndomain_of:\n- Biosample\nrange: string\n\nReference or method used in determining salinity
URI: MIXS:0000341
"},{"location":"salinity_meth/#inheritance","title":"Inheritance","text":"name: salinity_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining salinity\ntitle: salinity method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000341\nalias: salinity_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens
URI: MIXS:0000582
"},{"location":"salt_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: salt_regm\nannotations:\n expected_value:\n tag: expected_value\n value: salt name;salt amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of salts as supplement to liquid\n and soil growth media; should include the name of salt, amount administered, treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n salt regimens\ntitle: salt regimen\nexamples:\n- value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salt regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000582\nalias: salt_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nReason for the sample
URI: MIXS:0000860
"},{"location":"samp_capt_status/#inheritance","title":"Inheritance","text":"name: samp_capt_status\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reason for the sample\ntitle: sample capture status\nexamples:\n- value: farm sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample capture status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000860\nalias: samp_capt_status\ndomain_of:\n- Biosample\nrange: samp_capt_status_enum\nmultivalued: false\n\nThe device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
URI: MIXS:0000002
"},{"location":"samp_collec_device/#inheritance","title":"Inheritance","text":"name: samp_collec_device\nannotations:\n expected_value:\n tag: expected_value\n value: device name\ndescription: The device used to collect an environmental sample. This field accepts\n terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\ntitle: sample collection device\nexamples:\n- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection device\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000002\nalias: samp_collec_device\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe method employed for collecting the sample.
URI: MIXS:0001225
"},{"location":"samp_collec_method/#inheritance","title":"Inheritance","text":"name: samp_collec_method\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url , or text\ndescription: The method employed for collecting the sample.\ntitle: sample collection method\nexamples:\n- value: swabbing\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection method\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001225\nalias: samp_collec_method\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nSampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0001015
"},{"location":"samp_collect_point/#inheritance","title":"Inheritance","text":"name: samp_collect_point\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sampling point on the asset were sample was collected (e.g. Wellhead,\n storage tank, separator, etc). If \"other\" is specified, please propose entry in\n \"additional info\" field\ntitle: sample collection point\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001015\nalias: samp_collect_point\ndomain_of:\n- Biosample\nrange: samp_collect_point_enum\nmultivalued: false\n\nStage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.
URI: MIXS:0000249
"},{"location":"samp_dis_stage/#inheritance","title":"Inheritance","text":"name: samp_dis_stage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Stage of the disease at the time of sample collection, e.g. inoculation,\n penetration, infection, growth and reproduction, dissemination of pathogen.\ntitle: sample disease stage\nexamples:\n- value: infection\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample disease stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000249\nalias: samp_dis_stage\ndomain_of:\n- Biosample\nrange: samp_dis_stage_enum\nmultivalued: false\n\nThe floor of the building, where the sampling room is located
URI: MIXS:0000828
"},{"location":"samp_floor/#inheritance","title":"Inheritance","text":"name: samp_floor\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The floor of the building, where the sampling room is located\ntitle: sampling floor\nexamples:\n- value: 4th floor\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling floor\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000828\nalias: samp_floor\ndomain_of:\n- Biosample\nrange: samp_floor_enum\nmultivalued: false\n\nMetal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays
URI: MIXS:0000136
"},{"location":"samp_loc_corr_rate/#inheritance","title":"Inheritance","text":"name: samp_loc_corr_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: millimeter per year\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Metal corrosion rate is the speed of metal deterioration due to environmental\n conditions. As environmental conditions change corrosion rates change accordingly.\n Therefore, long term corrosion rates are generally more informative than short term\n rates and for that reason they are preferred during reporting. In the case of suspected\n MIC, corrosion rate measurements at the time of sampling might provide insights\n into the involvement of certain microbial community members in MIC as well as potential\n microbial interplays\ntitle: corrosion rate at sample location\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- corrosion rate at sample location\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000136\nalias: samp_loc_corr_rate\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.
URI: MIXS:0000016
"},{"location":"samp_mat_process/#inheritance","title":"Inheritance","text":"name: samp_mat_process\nannotations:\n expected_value:\n tag: expected_value\n value: text\ndescription: A brief description of any processing applied to the sample during or\n after retrieving the sample from environment, or a link to the relevant protocol(s)\n performed.\ntitle: sample material processing\nexamples:\n- value: filtering of seawater, storing samples in ethanol\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample material processing\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000016\nalias: samp_mat_process\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nIn non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000413
"},{"location":"samp_md/#inheritance","title":"Inheritance","text":"name: samp_md\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: In non deviated well, measured depth is equal to the true vertical depth,\n TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the\n MD is the length of trajectory of the borehole measured from the same reference\n or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary\n table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified,\n please propose entry in \"additional info\" field\ntitle: sample measured depth\nexamples:\n- value: 1534 meter;MSL\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample measured depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000413\nalias: samp_md\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nA local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.
URI: MIXS:0001107
"},{"location":"samp_name/#inheritance","title":"Inheritance","text":"name: samp_name\nannotations:\n expected_value:\n tag: expected_value\n value: text\ndescription: A local identifier or name that for the material sample used for extracting\n nucleic acids, and subsequent sequencing. It can refer either to the original material\n collected or to any derived sub-samples. It can have any format, but we suggest\n that you make it concise, unique and consistent within your lab, and as informative\n as possible. INSDC requires every sample name from a single Submitter to be unique.\n Use of a globally unique identifier for the field source_mat_id is recommended in\n addition to sample_name.\ntitle: sample name\nexamples:\n- value: ISDsoil1\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample name\nrank: 1000\nis_a: investigation field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001107\nalias: samp_name\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nPreservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)
URI: MIXS:0000463
"},{"location":"samp_preserv/#inheritance","title":"Inheritance","text":"name: samp_preserv\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliliter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\ntitle: preservative added to sample\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- preservative added to sample\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000463\nalias: samp_preserv\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSampling room number. This ID should be consistent with the designations on the building floor plans
URI: MIXS:0000244
"},{"location":"samp_room_id/#inheritance","title":"Inheritance","text":"name: samp_room_id\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sampling room number. This ID should be consistent with the designations\n on the building floor plans\ntitle: sampling room ID or name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling room ID or name\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000244\nalias: samp_room_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.
URI: MIXS:0000001
"},{"location":"samp_size/#inheritance","title":"Inheritance","text":"name: samp_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, liter\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n collected.\ntitle: amount or size of sample collected\nexamples:\n- value: 5 liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount or size of sample collected\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000001\nalias: samp_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMethod by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.
URI: MIXS:0000216
"},{"location":"samp_sort_meth/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: samp_sort_meth\nannotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: m\ndescription: Method by which samples are sorted; open face filter collecting total\n suspended particles, prefilter to remove particles larger than X micrometers in\n diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade\n impactor.\ntitle: sample size sorting method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample size sorting method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000216\nalias: samp_sort_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nDuration for which the sample was stored
URI: MIXS:0000116
"},{"location":"samp_store_dur/#inheritance","title":"Inheritance","text":"name: samp_store_dur\nannotations:\n expected_value:\n tag: expected_value\n value: duration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Duration for which the sample was stored\ntitle: sample storage duration\nexamples:\n- value: P1Y6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage duration\nrank: 1000\nis_a: core field\nstring_serialization: '{duration}'\nslot_uri: MIXS:0000116\nalias: samp_store_dur\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nLocation at which sample was stored, usually name of a specific freezer/room
URI: MIXS:0000755
"},{"location":"samp_store_loc/#inheritance","title":"Inheritance","text":"name: samp_store_loc\nannotations:\n expected_value:\n tag: expected_value\n value: location name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Location at which sample was stored, usually name of a specific freezer/room\ntitle: sample storage location\nexamples:\n- value: Freezer no:5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage location\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000755\nalias: samp_store_loc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nTemperature at which sample was stored, e.g. -80 degree Celsius
URI: MIXS:0000110
"},{"location":"samp_store_temp/#inheritance","title":"Inheritance","text":"name: samp_store_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature at which sample was stored, e.g. -80 degree Celsius\ntitle: sample storage temperature\nexamples:\n- value: -80 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000110\nalias: samp_store_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nName of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000999
"},{"location":"samp_subtype/#inheritance","title":"Inheritance","text":"name: samp_subtype\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of sample sub-type. For example if \"sample type\" is \"Produced Water\"\n then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please\n propose entry in \"additional info\" field\ntitle: sample subtype\nexamples:\n- value: biofilm\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample subtype\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000999\nalias: samp_subtype\ndomain_of:\n- Biosample\nrange: samp_subtype_enum\nmultivalued: false\n\nNCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample' for negative controls.
URI: MIXS:0001320
"},{"location":"samp_taxon_id/#inheritance","title":"Inheritance","text":"name: samp_taxon_id\nannotations:\n expected_value:\n tag: expected_value\n value: Taxonomy ID\ndescription: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample.\n Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample'\n for negative controls.\ntitle: Taxonomy ID of DNA sample\ncomments:\n- coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Taxonomy ID of DNA sample\nrank: 1000\nis_a: investigation field\nslot_uri: MIXS:0001320\nalias: samp_taxon_id\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nThe recent and long term history of outside sampling
URI: MIXS:0000196
"},{"location":"samp_time_out/#inheritance","title":"Inheritance","text":"name: samp_time_out\nannotations:\n expected_value:\n tag: expected_value\n value: time\n preferred_unit:\n tag: preferred_unit\n value: hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recent and long term history of outside sampling\ntitle: sampling time outside\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling time outside\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000196\nalias: samp_time_out\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)
URI: MIXS:0000410
"},{"location":"samp_transport_cond/#inheritance","title":"Inheritance","text":"name: samp_transport_cond\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: days;degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sample transport duration (in days or hrs) and temperature the sample\n was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\ntitle: sample transport conditions\nexamples:\n- value: 5 days;-20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample transport conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000410\nalias: samp_transport_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDepth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m
URI: MIXS:0000409
"},{"location":"samp_tvdss/#inheritance","title":"Inheritance","text":"name: samp_tvdss\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value or measurement value range\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Depth of the sample i.e. The vertical distance between the sea level\n and the sampled position in the subsurface. Depth can be reported as an interval\n for subsurface samples e.g. 1325.75-1362.25 m\ntitle: sample true vertical depth subsea\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample true vertical depth subsea\nrank: 1000\nis_a: core field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000409\nalias: samp_tvdss\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).
URI: MIXS:0000998
"},{"location":"samp_type/#inheritance","title":"Inheritance","text":"name: samp_type\nannotations:\n expected_value:\n tag: expected_value\n value: GENEPIO:0001246\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material from which the sample was obtained. For the Hydrocarbon\n package, samples include types like core, rock trimmings, drill cuttings, piping\n section, coupon, pigging debris, solid deposit, produced fluid, produced water,\n injected water, swabs, etc. For the Food Package, samples are usually categorized\n as food, body products or tissues, or environmental material. This field accepts\n terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\ntitle: sample type\nexamples:\n- value: built environment sample [GENEPIO:0001248]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000998\nalias: samp_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nVolume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).
URI: MIXS:0000111
"},{"location":"samp_vol_we_dna_ext/#inheritance","title":"Inheritance","text":"name: samp_vol_we_dna_ext\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, square centimeter\ndescription: 'Volume (ml) or mass (g) of total collected sample processed for DNA\n extraction. Note: total sample collected should be entered under the term Sample\n Size (MIXS:0000001).'\ntitle: sample volume or weight for DNA extraction\nexamples:\n- value: 1500 milliliter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample volume or weight for DNA extraction\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000111\nalias: samp_vol_we_dna_ext\nrange: QuantityValue\nmultivalued: false\n\nThe weather on the sampling day
URI: MIXS:0000827
"},{"location":"samp_weather/#inheritance","title":"Inheritance","text":"name: samp_weather\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The weather on the sampling day\ntitle: sampling day weather\nexamples:\n- value: foggy\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling day weather\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000827\nalias: samp_weather\ndomain_of:\n- Biosample\nrange: samp_weather_enum\nmultivalued: false\n\nName of the well (e.g. BXA1123) where sample was taken
URI: MIXS:0000296
"},{"location":"samp_well_name/#inheritance","title":"Inheritance","text":"name: samp_well_name\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the well (e.g. BXA1123) where sample was taken\ntitle: sample well name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample well name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000296\nalias: samp_well_name\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:sample_collection_day
"},{"location":"sample_collection_day/#properties","title":"Properties","text":"name: sample_collection_day\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_day\nrange: integer\n\nURI: nmdc:sample_collection_hour
"},{"location":"sample_collection_hour/#properties","title":"Properties","text":"name: sample_collection_hour\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_hour\nrange: integer\n\nURI: nmdc:sample_collection_minute
"},{"location":"sample_collection_minute/#properties","title":"Properties","text":"name: sample_collection_minute\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_minute\nrange: integer\n\nURI: nmdc:sample_collection_month
"},{"location":"sample_collection_month/#properties","title":"Properties","text":"name: sample_collection_month\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_month\nrange: string\n\nURI: nmdc:sample_collection_site
"},{"location":"sample_collection_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_collection_site/#properties","title":"Properties","text":"name: sample_collection_site\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_site\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:sample_collection_year
"},{"location":"sample_collection_year/#properties","title":"Properties","text":"name: sample_collection_year\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_year\nrange: integer\n\nA unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.
URI: nmdc:sample_link
"},{"location":"sample_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_link/#properties","title":"Properties","text":"Range: String
Multivalued: True
Recommended: True
name: sample_link\ndescription: A unique identifier to assign parent-child, subsample, or sibling samples.\n This is relevant when a sample or other material was used to generate the new sample.\ntitle: sample linkage\ncomments:\n- 'This field allows multiple entries separated by ; (Examples: Soil collected from\n the field will link with the soil used in an incubation. The soil a plant was grown\n in links to the plant sample. An original culture sample was transferred to a new\n vial and generated a new sample)'\nexamples:\n- value: IGSN:DSJ0284\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{text}:{text}'\nalias: sample_link\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: string\nrecommended: true\nmultivalued: true\n\nThe total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.
URI: nmdc:sample_shipped
"},{"location":"sample_shipped/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_shipped/#properties","title":"Properties","text":"Range: String
Recommended: True
name: sample_shipped\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n sent to EMSL.\ntitle: sample shipped amount\ncomments:\n- This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\nexamples:\n- value: 15 g\n- value: 100 uL\n- value: 5 mL\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{float} {unit}'\nalias: sample_shipped\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nThe chemical phase of a pure sample, or the state of a mixed sample
URI: nmdc:sample_state_information
"},{"location":"sample_state_information/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"sample_state_information/#properties","title":"Properties","text":"name: sample_state_information\ndescription: The chemical phase of a pure sample, or the state of a mixed sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_state_information\ndomain_of:\n- PortionOfSubstance\nrange: SampleStateEnum\n\nType of sample being submitted
URI: nmdc:sample_type
"},{"location":"sample_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_type/#properties","title":"Properties","text":"Range: SampleTypeEnum
Recommended: True
name: sample_type\ndescription: Type of sample being submitted\ntitle: sample type\ncomments:\n- This can vary from 'environmental package' if the sample is an extraction.\nexamples:\n- value: water extracted soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nalias: sample_type\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: SampleTypeEnum\nrecommended: true\n\nThe portion of the sample that is taken for downstream activity.
URI: nmdc:sampled_portion
"},{"location":"sampled_portion/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no"},{"location":"sampled_portion/#properties","title":"Properties","text":"Range: SamplePortionEnum
Multivalued: True
name: sampled_portion\ndescription: The portion of the sample that is taken for downstream activity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sampled_portion\ndomain_of:\n- SubSamplingProcess\nrange: SamplePortionEnum\nmultivalued: true\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000131
"},{"location":"saturates_pc/#inheritance","title":"Inheritance","text":"name: saturates_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: saturates wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- saturates wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000131\nalias: saturates_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nTotal size in bp of all scaffolds.
URI: nmdc:scaf_bp
"},{"location":"scaf_bp/#inheritance","title":"Inheritance","text":"name: scaf_bp\ndescription: Total size in bp of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.
URI: nmdc:scaf_l50
"},{"location":"scaf_l50/#inheritance","title":"Inheritance","text":"name: scaf_l50\ndescription: Given a set of scaffolds, the L50 is defined as the sequence length of\n the shortest scaffold at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.
URI: nmdc:scaf_l90
"},{"location":"scaf_l90/#inheritance","title":"Inheritance","text":"name: scaf_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n length for which the collection of all scaffolds of that length or longer contains\n at least 90% of the sum of the lengths of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal size in bp of all scaffolds greater than 50 KB.
URI: nmdc:scaf_l_gt50k
"},{"location":"scaf_l_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_l_gt50k\ndescription: Total size in bp of all scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase
URI: nmdc:scaf_logsum
"},{"location":"scaf_logsum/#inheritance","title":"Inheritance","text":"name: scaf_logsum\ndescription: The sum of the (length*log(length)) of all scaffolds, times some constant. Increase\n the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum scaffold length.
URI: nmdc:scaf_max
"},{"location":"scaf_max/#inheritance","title":"Inheritance","text":"name: scaf_max\ndescription: Maximum scaffold length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.
URI: nmdc:scaf_n50
"},{"location":"scaf_n50/#inheritance","title":"Inheritance","text":"name: scaf_n50\ndescription: Given a set of scaffolds, each with its own length, the N50 count is\n defined as the smallest number of scaffolds whose length sum makes up half of genome\n size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.
URI: nmdc:scaf_n90
"},{"location":"scaf_n90/#inheritance","title":"Inheritance","text":"name: scaf_n90\ndescription: Given a set of scaffolds, each with its own length, the N90 count is\n defined as the smallest number of scaffolds whose length sum makes up 90% of genome\n size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence count of scaffolds greater than 50 KB.
URI: nmdc:scaf_n_gt50k
"},{"location":"scaf_n_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_n_gt50k\ndescription: Total sequence count of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence size percentage of scaffolds greater than 50 KB.
URI: nmdc:scaf_pct_gt50k
"},{"location":"scaf_pct_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_pct_gt50k\ndescription: Total sequence size percentage of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_pct_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nPowersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
URI: nmdc:scaf_powsum
"},{"location":"scaf_powsum/#inheritance","title":"Inheritance","text":"name: scaf_powsum\ndescription: Powersum of all scaffolds is the same as logsum except that it uses the\n sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence count of all scaffolds.
URI: nmdc:scaffolds
"},{"location":"scaffolds/#inheritance","title":"Inheritance","text":"name: scaffolds\ndescription: Total sequence count of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaffolds\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe nmdc-schema's preferred serializations are YAML, closely followed by JSONSchema. MongoDB is the database of choice for storing data. The nmdc-schema is designed to be a bridge between these formats.
The nmdc-schema Makefiles use the linkml-validate and linkml-run-examples CLIs for build-time validation of data file, both of which build upon JSON Schema validation. linkml-validate can even validate against TSV, as long as the schema classes that are instantiated can reasonably be expressed in a table. Programmers can learn more about the internals of these tools at https://linkml.io/linkml/data/validating-data.html
We can conceive of validating a data file at two levels
All tools, libraries, or scripts generating NMDC data SHOULD instantiate Python data classes from the nmdc-schema PyPI package. It is strongly discouraged to generate Python dicts or JSON by any method other than object instantiation, even using high-quality, standard JSON libraries. That practice may generate valid data files when first tested but is likely to degrade over time. That degradation can be difficult to debug.
Mike Farrah's yq is a system dependency for the nmdc-schema. It can be used to validate legacy YAML and JSON data. If malformed YAML or JSON is presented to linkml-validate, the error messages may not be as helpful as the messages from yq or some other syntactical validator.
Start by reflecting on whether your data may be ahead of what the schema can currently account for.
For 1, you can make PR on the schema yaml. If you aren't comfortable editing LinkML YAML, then you can get help from one of the schema developers. We recommend filing a new ticket explaining the issue. Please include your error messages.
For 2, we suggest taking a minimal example approach. linkml-validate is very good at identifying schema violations in small, syntactically valid data files. Debugging can be aided in pulling out single data instances and first verifying that they are syntactically valid YAML or JSON. If you don't want to use yq, then you could paste one instance into a website like https://jsonlint.com/. A common issue in multi-instance files is using incorrect syntax for grouping the instances into a YAML or JSON array. Using a small subsample of your data and an online linter as above can aide in debugging this.
It is expected that data producers or transformers take the upfront initiative to validate their data.
Currently, not all providers of information to NMDC provide JSON - for example, GOLD is provided as database dumps, and an ETL process transforms this into JSON. In the future, we would like to move towards a situation where all information is provided as JSON.
"},{"location":"schema_element_deprecation_guide/","title":"Deprecating NMDC Schema elements","text":"By deprecating, rather than deleting, schema elements in the NMDC model, we ensure backward compatibility, extend user trust, and provide a valuable historical record, aiding in the understanding of the model's evolution. Therefore, 'deleting' a schema element in NMDC is instead, a two-step (and two-release) deprecation process.
"},{"location":"schema_element_deprecation_guide/#first-release-cycle","title":"First release cycle:","text":"# doi_awards deprecated on 2023-11-12 in a class's usage). * note: If a replacement is not warranted, then using only the deprecated metadata tag with an explanation string and issue link is fine.
** note: For a deprecated class, references could be in the is_a or mixin elements of another class, or in the domain or range elements of an existing slot. For deprecated slots, check all classes that reference that slot, etc.
Please see LinkML SchemaView documentation for general information. It has several good examples of how to use this module in a python script or from the command line. https://linkml.io/linkml/developers/schemaview.html#schemaview
There are also several notebooks that demonstrate SchemaView usage in the LinkML-runtime repository: https://github.com/linkml/linkml-runtime/tree/main/notebooks
"},{"location":"season/","title":"Slot: season (season)","text":"The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).
URI: MIXS:0000829
"},{"location":"season/#inheritance","title":"Inheritance","text":"name: season\nannotations:\n expected_value:\n tag: expected_value\n value: NCIT:C94729\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The season when sampling occurred. Any of the four periods into which\n the year is divided by the equinoxes and solstices. This field accepts terms listed\n under season (http://purl.obolibrary.org/obo/NCIT_C94729).\ntitle: season\nexamples:\n- value: autumn [NCIT:C94733]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- season\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000829\nalias: season\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nTreatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment
URI: MIXS:0001068
"},{"location":"season_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: season_environment\nannotations:\n expected_value:\n tag: expected_value\n value: seasonal environment name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to a particular season (e.g. Winter,\n summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment\ntitle: seasonal environment\nexamples:\n- value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001068\nalias: season_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.
URI: MIXS:0000645
"},{"location":"season_precpt/#inheritance","title":"Inheritance","text":"name: season_precpt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of all seasonal precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean seasonal precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000645\nalias: season_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMean seasonal temperature
URI: MIXS:0000643
"},{"location":"season_temp/#inheritance","title":"Inheritance","text":"name: season_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Mean seasonal temperature\ntitle: mean seasonal temperature\nexamples:\n- value: 18 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000643\nalias: season_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe seasons the space is occupied
URI: MIXS:0000830
"},{"location":"season_use/#inheritance","title":"Inheritance","text":"name: season_use\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The seasons the space is occupied\ntitle: seasonal use\nexamples:\n- value: Winter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000830\nalias: season_use\ndomain_of:\n- Biosample\nrange: season_use_enum\nmultivalued: false\n\nThe process for substantially degrading the biological content of the sewage
URI: MIXS:0000351
"},{"location":"secondary_treatment/#inheritance","title":"Inheritance","text":"name: secondary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: secondary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process for substantially degrading the biological content of the\n sewage\ntitle: secondary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000351\nalias: secondary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about the sediment type based on major constituents
URI: MIXS:0001078
"},{"location":"sediment_type/#inheritance","title":"Inheritance","text":"name: sediment_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about the sediment type based on major constituents\ntitle: sediment type\nexamples:\n- value: biogenous\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sediment type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001078\nalias: sediment_type\ndomain_of:\n- Biosample\nrange: sediment_type_enum\nmultivalued: false\n\nThe method that was used to separate a substance from a solution or mixture.
URI: nmdc:separation_method
"},{"location":"separation_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"separation_method/#properties","title":"Properties","text":"name: separation_method\ndescription: The method that was used to separate a substance from a solution or mixture.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: separation_method\ndomain_of:\n- FiltrationProcess\nrange: SeparationMethodEnum\n\nSequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).
URI: MIXS:0000050
"},{"location":"seq_meth/#inheritance","title":"Inheritance","text":"name: seq_meth\nannotations:\n expected_value:\n tag: expected_value\n value: Text or OBI\ndescription: Sequencing machine used. Where possible the term should be taken from\n the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\ntitle: sequencing method\nexamples:\n- value: 454 Genome Sequencer FLX [OBI:0000702]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequencing method\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000050\nalias: seq_meth\nrange: TextValue\nmultivalued: false\n\nIndicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA
URI: MIXS:0000051
"},{"location":"seq_quality_check/#inheritance","title":"Inheritance","text":"name: seq_quality_check\nannotations:\n expected_value:\n tag: expected_value\n value: none or manually edited\ndescription: Indicate if the sequence has been called by automatic systems (none)\n or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms).\n Applied only for sequences that are not submitted to SRA,ENA or DRA\ntitle: sequence quality check\nexamples:\n- value: none\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequence quality check\nrank: 1000\nis_a: sequencing field\nstring_serialization: '[none|manually edited]'\nslot_uri: MIXS:0000051\nalias: seq_quality_check\nrange: TextValue\nmultivalued: false\n\nThe ID of the landmark used to establish the coordinate system for the current feature.
URI: nmdc:seqid
"},{"location":"seqid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"seqid/#properties","title":"Properties","text":"name: seqid\ndescription: The ID of the landmark used to establish the coordinate system for the\n current feature.\ntodos:\n- change range from string to object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: seqid\ndomain_of:\n- GenomeFeature\nrange: string\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:sequencing_field
"},{"location":"sequencing_field/#inheritance","title":"Inheritance","text":"name: sequencing field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: sequencing_field\ndomain_of:\n- Biosample\nrange: string\n\nType of wastewater treatment plant as municipial or industrial
URI: MIXS:0000215
"},{"location":"sewage_type/#inheritance","title":"Inheritance","text":"name: sewage_type\nannotations:\n expected_value:\n tag: expected_value\n value: sewage type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Type of wastewater treatment plant as municipial or industrial\ntitle: sewage type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sewage type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000215\nalias: sewage_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSigns of the presence of mold or mildew on the shading device
URI: MIXS:0000834
"},{"location":"shad_dev_water_mold/#inheritance","title":"Inheritance","text":"name: shad_dev_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the shading device\ntitle: shading device signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000834\nalias: shad_dev_water_mold\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe physical condition of the shading device at the time of sampling
URI: MIXS:0000831
"},{"location":"shading_device_cond/#inheritance","title":"Inheritance","text":"name: shading_device_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the shading device at the time of sampling\ntitle: shading device condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000831\nalias: shading_device_cond\ndomain_of:\n- Biosample\nrange: shading_device_cond_enum\nmultivalued: false\n\nThe location of the shading device in relation to the built structure
URI: MIXS:0000832
"},{"location":"shading_device_loc/#inheritance","title":"Inheritance","text":"name: shading_device_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The location of the shading device in relation to the built structure\ntitle: shading device location\nexamples:\n- value: exterior\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device location\nrank: 1000\nis_a: core field\nstring_serialization: '[exterior|interior]'\nslot_uri: MIXS:0000832\nalias: shading_device_loc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe material the shading device is composed of
URI: MIXS:0000245
"},{"location":"shading_device_mat/#inheritance","title":"Inheritance","text":"name: shading_device_mat\nannotations:\n expected_value:\n tag: expected_value\n value: material name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material the shading device is composed of\ntitle: shading device material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device material\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000245\nalias: shading_device_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe type of shading device
URI: MIXS:0000835
"},{"location":"shading_device_type/#inheritance","title":"Inheritance","text":"name: shading_device_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of shading device\ntitle: shading device type\nexamples:\n- value: slatted aluminum awning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000835\nalias: shading_device_type\ndomain_of:\n- Biosample\nrange: shading_device_type_enum\nmultivalued: false\n\nCollection design of pooled samples and/or sieve size and amount of sample sieved
URI: MIXS:0000322
"},{"location":"sieving/#inheritance","title":"Inheritance","text":"name: sieving\nannotations:\n expected_value:\n tag: expected_value\n value: design name and/or size;amount\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Collection design of pooled samples and/or sieve size and amount of sample\n sieved\ntitle: composite design/sieving\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- composite design/sieving\nrank: 1000\nis_a: core field\nstring_serialization: '{{text}|{float} {unit}};{float} {unit}'\nslot_uri: MIXS:0000322\nalias: sieving\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of silicate
URI: MIXS:0000184
"},{"location":"silicate/#inheritance","title":"Inheritance","text":"name: silicate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of silicate\ntitle: silicate\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- silicate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000184\nalias: silicate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nFiltering pore size used in sample preparation
URI: MIXS:0000017
"},{"location":"size_frac/#inheritance","title":"Inheritance","text":"name: size_frac\nannotations:\n expected_value:\n tag: expected_value\n value: filter size value range\ndescription: Filtering pore size used in sample preparation\ntitle: size fraction selected\nexamples:\n- value: 0-0.22 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size fraction selected\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000017\nalias: size_frac\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nRefers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample
URI: MIXS:0000735
"},{"location":"size_frac_low/#inheritance","title":"Inheritance","text":"name: size_frac_low\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n Materials larger than the size threshold are excluded from the sample\ntitle: size-fraction lower threshold\nexamples:\n- value: 0.2 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction lower threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000735\nalias: size_frac_low\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nRefers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample
URI: MIXS:0000736
"},{"location":"size_frac_up/#inheritance","title":"Inheritance","text":"name: size_frac_up\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the mesh/pore size used to retain the sample. Materials smaller\n than the size threshold are excluded from the sample\ntitle: size-fraction upper threshold\nexamples:\n- value: 20 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction upper threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000736\nalias: size_frac_up\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.
URI: MIXS:0000647
"},{"location":"slope_aspect/#inheritance","title":"Inheritance","text":"name: slope_aspect\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees.\n This measure provides an indication of sun and wind exposure that will influence\n soil temperature and evapotranspiration.\ntitle: slope aspect\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope aspect\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000647\nalias: slope_aspect\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCommonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer
URI: MIXS:0000646
"},{"location":"slope_gradient/#inheritance","title":"Inheritance","text":"name: slope_gradient\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Commonly called 'slope'. The angle between ground surface and a horizontal\n line (in percent). This is the direction that overland water would flow. This measure\n is usually taken with a hand level meter or clinometer\ntitle: slope gradient\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope gradient\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000646\nalias: slope_gradient\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe time activated sludge remains in reactor
URI: MIXS:0000669
"},{"location":"sludge_retent_time/#inheritance","title":"Inheritance","text":"name: sludge_retent_time\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: hours\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The time activated sludge remains in reactor\ntitle: sludge retention time\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sludge retention time\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000669\nalias: sludge_retent_time\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nA string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.
URI: nmdc:smiles
"},{"location":"smiles/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: smiles\ndescription: A string encoding of a molecular graph, no chiral or isotopic information.\n There are usually a large number of valid SMILES which represent a given structure.\n For example, CCO, OCC and C(O)C all specify the structure of ethanol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: smiles\nrange: string\nmultivalued: true\n\nSodium concentration in the sample
URI: MIXS:0000428
"},{"location":"sodium/#inheritance","title":"Inheritance","text":"name: sodium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sodium concentration in the sample\ntitle: sodium\nexamples:\n- value: 10.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sodium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000428\nalias: sodium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:soil_annual_season_temp
"},{"location":"soil_annual_season_temp/#properties","title":"Properties","text":"name: soil_annual_season_temp\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soil_annual_season_temp\nrange: string\n\nSpecific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath
URI: MIXS:0001082
"},{"location":"soil_horizon/#inheritance","title":"Inheritance","text":"name: soil_horizon\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specific layer in the land area which measures parallel to the soil surface\n and possesses physical characteristics which differ from the layers above and beneath\ntitle: soil horizon\nexamples:\n- value: A horizon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001082\nalias: soil_horizon\ndomain_of:\n- Biosample\nrange: soil_horizon_enum\nmultivalued: false\n\nThe relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.
URI: MIXS:0000335
"},{"location":"soil_text_measure/#inheritance","title":"Inheritance","text":"name: soil_text_measure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative proportion of different grain sizes of mineral particles\n in a soil, as described using a standard system; express as % sand (50 um to 2 mm),\n silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam)\n optional.\ntitle: soil texture measurement\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture measurement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000335\nalias: soil_text_measure\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining soil texture
URI: MIXS:0000336
"},{"location":"soil_texture_meth/#inheritance","title":"Inheritance","text":"name: soil_texture_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining soil texture\ntitle: soil texture method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000336\nalias: soil_texture_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nDescription of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.
URI: MIXS:0000332
"},{"location":"soil_type/#inheritance","title":"Inheritance","text":"name: soil_type\nannotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of the soil type or classification. This field accepts terms\n under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be\n separated by pipes.\ntitle: soil type\nexamples:\n- value: plinthosol [ENVO:00002250]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000332\nalias: soil_type\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\nReference or method used in determining soil series name or other lower-level classification
URI: MIXS:0000334
"},{"location":"soil_type_meth/#inheritance","title":"Inheritance","text":"name: soil_type_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining soil series name or other lower-level\n classification\ntitle: soil type method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000334\nalias: soil_type_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe amount of solar energy that arrives at a specific area of a surface during a specific time interval
URI: MIXS:0000112
"},{"location":"solar_irradiance/#inheritance","title":"Inheritance","text":"name: solar_irradiance\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatts per square meter per day, ergs per square centimeter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The amount of solar energy that arrives at a specific area of a surface\n during a specific time interval\ntitle: solar irradiance\nexamples:\n- value: 1.36 kilowatts per square meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- solar irradiance\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000112\nalias: solar_irradiance\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
URI: MIXS:0000672
"},{"location":"soluble_inorg_mat/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: soluble_inorg_mat\nannotations:\n expected_value:\n tag: expected_value\n value: soluble inorganic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide,\n hydrogen sulfide, thiocyanates, thiosulfates, etc.\ntitle: soluble inorganic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble inorganic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000672\nalias: soluble_inorg_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:soluble_iron_micromol
"},{"location":"soluble_iron_micromol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_iron_micromol/#properties","title":"Properties","text":"name: soluble_iron_micromol\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soluble_iron_micromol\ndomain_of:\n- Biosample\nrange: string\n\nConcentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.
URI: MIXS:0000673
"},{"location":"soluble_org_mat/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: soluble_org_mat\nannotations:\n expected_value:\n tag: expected_value\n value: soluble organic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances such as urea, fruit sugars, soluble proteins,\n drugs, pharmaceuticals, etc.\ntitle: soluble organic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble organic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000673\nalias: soluble_org_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of soluble reactive phosphorus
URI: MIXS:0000738
"},{"location":"soluble_react_phosp/#inheritance","title":"Inheritance","text":"name: soluble_react_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of soluble reactive phosphorus\ntitle: soluble reactive phosphorus\nexamples:\n- value: 0.1 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble reactive phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000738\nalias: soluble_react_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nWhen solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in solution A
URI: nmdc:source_concentration
"},{"location":"source_concentration/#inheritance","title":"Inheritance","text":"name: source_concentration\ndescription: When solutions A (containing substance X) and B are combined together,\n this slot captures the concentration of X in solution A\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: concentration\nalias: source_concentration\ndomain_of:\n- PortionOfSubstance\nrange: QuantityValue\n\nA unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).
URI: MIXS:0000026
"},{"location":"source_mat_id/#inheritance","title":"Inheritance","text":"name: source_mat_id\nannotations:\n expected_value:\n tag: expected_value\n value: 'for cultures of microorganisms: identifiers for two culture collections;\n for other material a unique arbitrary identifer'\ndescription: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID,\n and as opposed to a particular digital record of a material sample) used for extracting\n nucleic acids, and subsequent sequencing. The identifier can refer either to the\n original material collected or to any derived sub-samples. The INSDC qualifiers\n /specimen_voucher, /bio_material, or /culture_collection may or may not share the\n same value as the source_mat_id field. For instance, the /specimen_voucher qualifier\n and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen\n voucher and sampled tissue with the same identifier. However, the /culture_collection\n qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id\n would refer to an identifier from some derived culture from which the nucleic acids\n were extracted (e.g. xatc123 or ark:/2154/R2).\ntitle: source material identifiers\nexamples:\n- value: MPI012345\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source material identifiers\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000026\nalias: source_mat_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nCustomary or normal state of the space
URI: MIXS:0000770
"},{"location":"space_typ_state/#inheritance","title":"Inheritance","text":"name: space_typ_state\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Customary or normal state of the space\ntitle: space typical state\nexamples:\n- value: typically occupied\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- space typical state\nrank: 1000\nis_a: core field\nstring_serialization: '[typically occupied|typically unoccupied]'\nslot_uri: MIXS:0000770\nalias: space_typ_state\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents
URI: MIXS:0000836
"},{"location":"specific/#inheritance","title":"Inheritance","text":"name: specific\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'The building specifications. If design is chosen, indicate phase: conceptual,\n schematic, design development, construction documents'\ntitle: specifications\nexamples:\n- value: construction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specifications\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000836\nalias: specific\ndomain_of:\n- Biosample\nrange: specific_enum\nmultivalued: false\n\nSpecific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.
URI: nmdc:specific_ecosystem
"},{"location":"specific_ecosystem/#inheritance","title":"Inheritance","text":"name: specific_ecosystem\ndescription: Specific ecosystems represent specific features of the environment like\n aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific\n ecosystem is in position 5/5 in a GOLD path.\ncomments:\n- Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: specific_ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nThe mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.
URI: MIXS:0000214
"},{"location":"specific_humidity/#inheritance","title":"Inheritance","text":"name: specific_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The mass of water vapour in a unit mass of moist air, usually expressed\n as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.\ntitle: specific humidity\nexamples:\n- value: 15 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specific humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000214\nalias: specific_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSource rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000996
"},{"location":"sr_dep_env/#inheritance","title":"Inheritance","text":"name: sr_dep_env\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock depositional environment\nexamples:\n- value: Marine\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000996\nalias: sr_dep_env\ndomain_of:\n- Biosample\nrange: sr_dep_env_enum\nmultivalued: false\n\nGeological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000997
"},{"location":"sr_geol_age/#inheritance","title":"Inheritance","text":"name: sr_geol_age\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: source rock geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000997\nalias: sr_geol_age\ndomain_of:\n- Biosample\nrange: sr_geol_age_enum\nmultivalued: false\n\nOrigin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000994
"},{"location":"sr_kerog_type/#inheritance","title":"Inheritance","text":"name: sr_kerog_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and\n soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous\n plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial)\n (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified,\n please propose entry in \"additional info\" field'\ntitle: source rock kerogen type\nexamples:\n- value: Type IV\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock kerogen type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000994\nalias: sr_kerog_type\ndomain_of:\n- Biosample\nrange: sr_kerog_type_enum\nmultivalued: false\n\nLithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000995
"},{"location":"sr_lithology/#inheritance","title":"Inheritance","text":"name: sr_lithology\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock lithology\nexamples:\n- value: Coal\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000995\nalias: sr_lithology\ndomain_of:\n- Biosample\nrange: sr_lithology_enum\nmultivalued: false\n\nTreatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0001069
"},{"location":"standing_water_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: standing_water_regm\nannotations:\n expected_value:\n tag: expected_value\n value: standing water type;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to standing water during a plant's life\n span, types can be flood water or standing water, treatment regimen including how\n many times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple regimens\ntitle: standing water regimen\nexamples:\n- value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- standing water regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001069\nalias: standing_water_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe start of the feature in positive 1-based integer coordinates
URI: nmdc:start
"},{"location":"start/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: start\ndescription: The start of the feature in positive 1-based integer coordinates\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:start_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: start\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\nThe date on which any process or activity was started
URI: nmdc:start_date
"},{"location":"start_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no FiltrationProcess The process of segregation of phases; e no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAnnotation no NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no LibraryPreparation no StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no WorkflowExecution Represents an instance of an execution of a particular workflow no Extraction A material separation in which a desired component of an input material is se... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ProtocolExecution A PlannedProces that has PlannedProcess parts no MetaproteomicsAnalysis no PlannedProcess no"},{"location":"start_date/#properties","title":"Properties","text":"name: start_date\ndescription: The date on which any process or activity was started\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: start_date\ndomain_of:\n- PlannedProcess\nrange: string\n\nDate the incubation was started. Only relevant for incubation samples.
URI: nmdc:start_date_inc
"},{"location":"start_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_date_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: start_date_inc\ndescription: Date the incubation was started. Only relevant for incubation samples.\ntitle: incubation start date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n all acceptable.\nexamples:\n- value: '2021-04-15'\n- value: 2021-04\n- value: '2021'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 4\nstring_serialization: '{date, arbitrary precision}'\nalias: start_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nTime the incubation was started. Only relevant for incubation samples.
URI: nmdc:start_time_inc
"},{"location":"start_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_time_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: start_time_inc\ndescription: Time the incubation was started. Only relevant for incubation samples.\ntitle: incubation start time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: '13:33'\n- value: '13:33:55'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 5\nstring_serialization: '{time, seconds optional}'\nalias: start_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nURI: nmdc:started_at_time
"},{"location":"started_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NomAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAnnotation no MetaproteomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow yes"},{"location":"started_at_time/#properties","title":"Properties","text":"Range: String
Regex pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$
name: started_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:startedAtTime\nrank: 1000\nalias: started_at_time\ndomain_of:\n- WorkflowExecution\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\nThe material the stationary phase is comprised of used in chromatography.
URI: nmdc:stationary_phase
"},{"location":"stationary_phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no"},{"location":"stationary_phase/#properties","title":"Properties","text":"name: stationary_phase\ndescription: The material the stationary phase is comprised of used in chromatography.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stationary_phase\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: StationaryPhaseEnum\n\nThis property links a database object to the set of storage processes within it.
URI: nmdc:storage_process_set
"},{"location":"storage_process_set/#inheritance","title":"Inheritance","text":"Range: StorageProcess
Multivalued: True
name: storage_process_set\ndescription: This property links a database object to the set of storage processes\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: storage_process_set\ndomain_of:\n- Database\nrange: StorageProcess\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nExplain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).
URI: MIXS:0000327
"},{"location":"store_cond/#inheritance","title":"Inheritance","text":"name: store_cond\nannotations:\n expected_value:\n tag: expected_value\n value: storage condition type;duration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Explain how and for how long the soil sample was stored before DNA extraction\n (fresh/frozen/other).\ntitle: storage conditions\nexamples:\n- value: -20 degree Celsius freezer;P2Y10D\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- storage conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000327\nalias: store_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).
URI: nmdc:strand
"},{"location":"strand/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"strand/#properties","title":"Properties","text":"name: strand\ndescription: The strand on which a feature is located. Has a value of '+' (sense strand\n or forward strand) or '-' (anti-sense strand or reverse strand).\ntodos:\n- set the range to an enum?\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:strand\nrank: 1000\nalias: strand\ndomain_of:\n- GenomeFeature\nrange: string\n\nLists the strand orientiation for a stranded RNA library preparation.
URI: nmdc:stranded_orientation
"},{"location":"stranded_orientation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"stranded_orientation/#properties","title":"Properties","text":"name: stranded_orientation\ndescription: Lists the strand orientiation for a stranded RNA library preparation.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stranded_orientation\ndomain_of:\n- LibraryPreparation\nrange: StrandedOrientationEnum\n\nThe type of research initiative
URI: nmdc:study_category
"},{"location":"study_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_category/#properties","title":"Properties","text":"Range: StudyCategoryEnum
Required: True
name: study_category\ndescription: The type of research initiative\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_category\ndomain_of:\n- Study\nrange: StudyCategoryEnum\nrequired: true\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:study_identifiers
"},{"location":"study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: study_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nLinks a study to one or more images.
URI: nmdc:study_image
"},{"location":"study_image/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_image/#properties","title":"Properties","text":"Range: ImageValue
Multivalued: True
name: study_image\ndescription: Links a study to one or more images.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_image\ndomain_of:\n- Study\nrange: ImageValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of studies within it.
URI: nmdc:study_set
"},{"location":"study_set/#inheritance","title":"Inheritance","text":"Range: Study
Multivalued: True
name: study_set\ndescription: This property links a database object to the set of studies within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: study_set\ndomain_of:\n- Database\nrange: Study\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:subject
"},{"location":"subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e no OntologyRelation A relationship between two ontology classes as specified either directly in t... no"},{"location":"subject/#properties","title":"Properties","text":"name: subject\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subject\ndomain_of:\n- FunctionalAnnotation\n- OntologyRelation\nrange: GeneProduct\n\nThe role of a substance in a process
URI: nmdc:substance_role
"},{"location":"substance_role/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"substance_role/#properties","title":"Properties","text":"name: substance_role\ndescription: The role of a substance in a process\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substance_role\ndomain_of:\n- PortionOfSubstance\nrange: SubstanceRoleEnum\n\nThe substances that are combined to enable a ChemicalConversionProcess.
URI: nmdc:substances_used
"},{"location":"substances_used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no StorageProcess A planned process with the objective to preserve and protect material entitie... yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no"},{"location":"substances_used/#properties","title":"Properties","text":"Range: PortionOfSubstance
Multivalued: True
name: substances_used\ndescription: The substances that are combined to enable a ChemicalConversionProcess.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substances_used\ndomain_of:\n- Extraction\n- StorageProcess\n- DissolvingProcess\n- ChemicalConversionProcess\n- MobilePhaseSegment\nrange: PortionOfSubstance\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe volume of the combined substances that was included in a ChemicalConversionProcess.
URI: nmdc:substances_volume
"},{"location":"substances_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no"},{"location":"substances_volume/#properties","title":"Properties","text":"name: substances_volume\ndescription: The volume of the combined substances that was included in a ChemicalConversionProcess.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substances_volume\ndomain_of:\n- ChemicalConversionProcess\nrange: QuantityValue\n\nThe substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level
URI: MIXS:0000767
"},{"location":"substructure_type/#inheritance","title":"Inheritance","text":"Range: SubstructureTypeEnum
Multivalued: True
name: substructure_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: The substructure or under building is that largely hidden section of\n the building which is built off the foundations to the ground floor level\ntitle: substructure type\nexamples:\n- value: basement\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- substructure type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000767\nalias: substructure_type\ndomain_of:\n- Biosample\nrange: substructure_type_enum\nmultivalued: true\n\nURI: nmdc:subsurface_depth
"},{"location":"subsurface_depth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"subsurface_depth/#properties","title":"Properties","text":"name: subsurface_depth\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subsurface_depth\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of sulfate in the sample
URI: MIXS:0000423
"},{"location":"sulfate/#inheritance","title":"Inheritance","text":"name: sulfate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of sulfate in the sample\ntitle: sulfate\nexamples:\n- value: 5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000423\nalias: sulfate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nOriginal sulfate concentration in the hydrocarbon resource
URI: MIXS:0000407
"},{"location":"sulfate_fw/#inheritance","title":"Inheritance","text":"name: sulfate_fw\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original sulfate concentration in the hydrocarbon resource\ntitle: sulfate in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000407\nalias: sulfate_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of sulfide in the sample
URI: MIXS:0000424
"},{"location":"sulfide/#inheritance","title":"Inheritance","text":"name: sulfide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of sulfide in the sample\ntitle: sulfide\nexamples:\n- value: 2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000424\nalias: sulfide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nContaminant identified on surface
URI: MIXS:0000759
"},{"location":"surf_air_cont/#inheritance","title":"Inheritance","text":"Range: SurfAirContEnum
Multivalued: True
name: surf_air_cont\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Contaminant identified on surface\ntitle: surface-air contaminant\nexamples:\n- value: radon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface-air contaminant\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000759\nalias: surf_air_cont\ndomain_of:\n- Biosample\nrange: surf_air_cont_enum\nmultivalued: true\n\nSurfaces: water activity as a function of air and material moisture
URI: MIXS:0000123
"},{"location":"surf_humidity/#inheritance","title":"Inheritance","text":"name: surf_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Surfaces: water activity as a function of air and material moisture'\ntitle: surface humidity\nexamples:\n- value: 10%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000123\nalias: surf_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSurface materials at the point of sampling
URI: MIXS:0000758
"},{"location":"surf_material/#inheritance","title":"Inheritance","text":"name: surf_material\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Surface materials at the point of sampling\ntitle: surface material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000758\nalias: surf_material\ndomain_of:\n- Biosample\nrange: surf_material_enum\nmultivalued: false\n\nWater held on a surface
URI: MIXS:0000128
"},{"location":"surf_moisture/#inheritance","title":"Inheritance","text":"name: surf_moisture\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million, gram per cubic meter, gram per square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water held on a surface\ntitle: surface moisture\nexamples:\n- value: 0.01 gram per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000128\nalias: surf_moisture\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nph measurement of surface
URI: MIXS:0000760
"},{"location":"surf_moisture_ph/#inheritance","title":"Inheritance","text":"name: surf_moisture_ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: ph measurement of surface\ntitle: surface moisture pH\nexamples:\n- value: '7'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000760\nalias: surf_moisture_ph\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\nTemperature of the surface at the time of sampling
URI: MIXS:0000125
"},{"location":"surf_temp/#inheritance","title":"Inheritance","text":"name: surf_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature of the surface at the time of sampling\ntitle: surface temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000125\nalias: surf_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of suspended particulate matter
URI: MIXS:0000741
"},{"location":"suspend_part_matter/#inheritance","title":"Inheritance","text":"name: suspend_part_matter\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of suspended particulate matter\ntitle: suspended particulate matter\nexamples:\n- value: 0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended particulate matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000741\nalias: suspend_part_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances
URI: MIXS:0000150
"},{"location":"suspend_solids/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: suspend_solids\nannotations:\n expected_value:\n tag: expected_value\n value: suspended solid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, milligram per liter, mole per liter, gram per liter, part\n per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances including a wide variety of material, such\n as silt, decaying plant and animal matter; can include multiple substances\ntitle: suspended solids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended solids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000150\nalias: suspend_solids\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTotal Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)
URI: MIXS:0000120
"},{"location":"tan/#inheritance","title":"Inheritance","text":"name: tan\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\ntitle: total acid number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total acid number\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000120\nalias: tan\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTargeted gene or locus name for marker gene studies
URI: MIXS:0000044
"},{"location":"target_gene/#inheritance","title":"Inheritance","text":"name: target_gene\nannotations:\n expected_value:\n tag: expected_value\n value: gene name\ndescription: Targeted gene or locus name for marker gene studies\ntitle: target gene\nexamples:\n- value: 16S rRNA, 18S rRNA, nif, amoA, rpo\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target gene\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000044\nalias: target_gene\ndomain_of:\n- NucleotideSequencing\nrange: TargetGeneEnum\nmultivalued: false\n\nName of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA
URI: MIXS:0000045
"},{"location":"target_subfragment/#inheritance","title":"Inheritance","text":"name: target_subfragment\nannotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\ndescription: Name of subfragment of a gene or locus. Important to e.g. identify special\n regions on marker genes like V6 on 16S rRNA\ntitle: target subfragment\nexamples:\n- value: V6, V9, ITS\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target subfragment\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000045\nalias: target_subfragment\ndomain_of:\n- NucleotideSequencing\nrange: TextValue\nmultivalued: false\n\nIf sending technical replicates of the same sample, indicate the replicate count.
URI: nmdc:technical_reps
"},{"location":"technical_reps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"technical_reps/#properties","title":"Properties","text":"Range: String
Recommended: True
name: technical_reps\ndescription: If sending technical replicates of the same sample, indicate the replicate\n count.\ntitle: number technical replicate\ncomments:\n- This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{integer}'\nalias: technical_reps\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nTemperature of the sample at the time of sampling.
URI: MIXS:0000113
"},{"location":"temp/#inheritance","title":"Inheritance","text":"name: temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\ndescription: Temperature of the sample at the time of sampling.\ntitle: temperature\nexamples:\n- value: 25 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000113\nalias: temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe recorded temperature value at sampling time outside
URI: MIXS:0000197
"},{"location":"temp_out/#inheritance","title":"Inheritance","text":"name: temp_out\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded temperature value at sampling time outside\ntitle: temperature outside house\nexamples:\n- value: 5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature outside house\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000197\nalias: temp_out\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe value of a temperature measurement or temperature used in a process.
URI: nmdc:temperature
"},{"location":"temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no StorageProcess A planned process with the objective to preserve and protect material entitie... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no"},{"location":"temperature/#properties","title":"Properties","text":"name: temperature\ndescription: The value of a temperature measurement or temperature used in a process.\nnotes:\n- Not to be confused with the MIXS:0000113\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: temperature\ndomain_of:\n- ChromatographyConfiguration\n- SubSamplingProcess\n- StorageProcess\n- ChromatographicSeparationProcess\n- DissolvingProcess\n- ChemicalConversionProcess\nrange: QuantityValue\n\npointer to an ontology class
URI: nmdc:term
"},{"location":"term/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ControlledTermValue A controlled term or class from an ontology no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... yes"},{"location":"term/#properties","title":"Properties","text":"name: term\ndescription: pointer to an ontology class\nnotes:\n- 'removed ''slot_uri: rdf:type'''\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: term\ndomain_of:\n- ControlledTermValue\nrange: OntologyClass\ninlined: true\n\nThe process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment
URI: MIXS:0000352
"},{"location":"tertiary_treatment/#inheritance","title":"Inheritance","text":"name: tertiary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: tertiary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process providing a final treatment stage to raise the effluent quality\n before it is discharged to the receiving environment\ntitle: tertiary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tertiary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000352\nalias: tertiary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nStage of tide
URI: MIXS:0000750
"},{"location":"tidal_stage/#inheritance","title":"Inheritance","text":"name: tidal_stage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Stage of tide\ntitle: tidal stage\nexamples:\n- value: high tide\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tidal stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000750\nalias: tidal_stage\ndomain_of:\n- Biosample\nrange: tidal_stage_enum\nmultivalued: false\n\nNote method(s) used for tilling
URI: MIXS:0001081
"},{"location":"tillage/#inheritance","title":"Inheritance","text":"Range: TillageEnum
Multivalued: True
name: tillage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Note method(s) used for tilling\ntitle: history/tillage\nexamples:\n- value: chisel\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/tillage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001081\nalias: tillage\ndomain_of:\n- Biosample\nrange: tillage_enum\nmultivalued: true\n\nDescription of plant tissue culture growth media used
URI: MIXS:0001070
"},{"location":"tiss_cult_growth_med/#inheritance","title":"Inheritance","text":"name: tiss_cult_growth_med\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of plant tissue culture growth media used\ntitle: tissue culture growth media\nexamples:\n- value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tissue culture growth media\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001070\nalias: tiss_cult_growth_med\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.
URI: nmdc:title
"},{"location":"title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"title/#properties","title":"Properties","text":"name: title\ndescription: A name given to the entity that differs from the name/label programmatically\n assigned to it. For example, when extracting study information for GOLD, the GOLD\n system has assigned a name/label. However, for display purposes, we may also wish\n the capture the title of the proposal that was used to fund the study.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:title\nrank: 1000\nalias: title\ndomain_of:\n- Study\nrange: string\n\nConcentration of toluene in the sample
URI: MIXS:0000154
"},{"location":"toluene/#inheritance","title":"Inheritance","text":"name: toluene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of toluene in the sample\ntitle: toluene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- toluene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000154\nalias: toluene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nNumber of contigs which were excluded from binning for length.
URI: nmdc:too_short_contig_num
"},{"location":"too_short_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"too_short_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: too_short_contig_num\ndescription: Number of contigs which were excluded from binning for length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: too_short_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nTotal carbon content
URI: MIXS:0000525
"},{"location":"tot_carb/#inheritance","title":"Inheritance","text":"name: tot_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total carbon content\ntitle: total carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000525\nalias: tot_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of total depth of water column
URI: MIXS:0000634
"},{"location":"tot_depth_water_col/#inheritance","title":"Inheritance","text":"name: tot_depth_water_col\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of total depth of water column\ntitle: total depth of water column\nexamples:\n- value: 500 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total depth of water column\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000634\nalias: tot_depth_water_col\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen
URI: MIXS:0000744
"},{"location":"tot_diss_nitro/#inheritance","title":"Inheritance","text":"name: tot_diss_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\ntitle: total dissolved nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total dissolved nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000744\nalias: tot_diss_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal inorganic nitrogen content
URI: MIXS:0000745
"},{"location":"tot_inorg_nitro/#inheritance","title":"Inheritance","text":"name: tot_inorg_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total inorganic nitrogen content\ntitle: total inorganic nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000745\nalias: tot_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of total iron in the sample
URI: MIXS:0000105
"},{"location":"tot_iron/#inheritance","title":"Inheritance","text":"name: tot_iron\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, milligram per kilogram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of total iron in the sample\ntitle: total iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000105\nalias: tot_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen
URI: MIXS:0000102
"},{"location":"tot_nitro/#inheritance","title":"Inheritance","text":"name: tot_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total nitrogen concentration of water samples, calculated by: total\n nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n without filtering, reported as nitrogen'\ntitle: total nitrogen concentration\nexamples:\n- value: 50 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen concentration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000102\nalias: tot_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining the total nitrogen
URI: MIXS:0000338
"},{"location":"tot_nitro_cont_meth/#inheritance","title":"Inheritance","text":"name: tot_nitro_cont_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the total nitrogen\ntitle: total nitrogen content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000338\nalias: tot_nitro_cont_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nTotal nitrogen content of the sample
URI: MIXS:0000530
"},{"location":"tot_nitro_content/#inheritance","title":"Inheritance","text":"name: tot_nitro_content\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total nitrogen content of the sample\ntitle: total nitrogen content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000530\nalias: tot_nitro_content\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining total organic carbon
URI: MIXS:0000337
"},{"location":"tot_org_c_meth/#inheritance","title":"Inheritance","text":"name: tot_org_c_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining total organic carbon\ntitle: total organic carbon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000337\nalias: tot_org_c_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDefinition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content
URI: MIXS:0000533
"},{"location":"tot_org_carb/#inheritance","title":"Inheritance","text":"name: tot_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram Carbon per kilogram sample material\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Definition for soil: total organic carbon content of the soil, definition\n otherwise: total organic carbon content'\ntitle: total organic carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000533\nalias: tot_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal particulate carbon content
URI: MIXS:0000747
"},{"location":"tot_part_carb/#inheritance","title":"Inheritance","text":"name: tot_part_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total particulate carbon content\ntitle: total particulate carbon\nexamples:\n- value: 35 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total particulate carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000747\nalias: tot_part_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus
URI: MIXS:0000117
"},{"location":"tot_phosp/#inheritance","title":"Inheritance","text":"name: tot_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total phosphorus concentration in the sample, calculated by: total phosphorus\n = total dissolved phosphorus + particulate phosphorus'\ntitle: total phosphorus\nexamples:\n- value: 0.03 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000117\nalias: tot_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal amount or concentration of phosphate
URI: MIXS:0000689
"},{"location":"tot_phosphate/#inheritance","title":"Inheritance","text":"name: tot_phosphate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total amount or concentration of phosphate\ntitle: total phosphate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000689\nalias: tot_phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of total sulfur in the sample
URI: MIXS:0000419
"},{"location":"tot_sulfur/#inheritance","title":"Inheritance","text":"name: tot_sulfur\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of total sulfur in the sample\ntitle: total sulfur\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total sulfur\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000419\nalias: tot_sulfur\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal number of basepairs.
URI: nmdc:total_bases
"},{"location":"total_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"total_bases/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: total_bases\ndescription: Total number of basepairs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: total_bases\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nThe subway line name
URI: MIXS:0000837
"},{"location":"train_line/#inheritance","title":"Inheritance","text":"name: train_line\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The subway line name\ntitle: train line\nexamples:\n- value: red\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train line\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000837\nalias: train_line\ndomain_of:\n- Biosample\nrange: train_line_enum\nmultivalued: false\n\nThe train station collection location
URI: MIXS:0000838
"},{"location":"train_stat_loc/#inheritance","title":"Inheritance","text":"name: train_stat_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The train station collection location\ntitle: train station collection location\nexamples:\n- value: forest hills\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train station collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000838\nalias: train_stat_loc\ndomain_of:\n- Biosample\nrange: train_stat_loc_enum\nmultivalued: false\n\nThe train stop collection location
URI: MIXS:0000839
"},{"location":"train_stop_loc/#inheritance","title":"Inheritance","text":"name: train_stop_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The train stop collection location\ntitle: train stop collection location\nexamples:\n- value: end\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train stop collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000839\nalias: train_stop_loc\ndomain_of:\n- Biosample\nrange: train_stop_loc_enum\nmultivalued: false\n\nMeasure of the amount of cloudiness or haziness in water caused by individual particles
URI: MIXS:0000191
"},{"location":"turbidity/#inheritance","title":"Inheritance","text":"name: turbidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: formazin turbidity unit, formazin nephelometric units\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measure of the amount of cloudiness or haziness in water caused by individual\n particles\ntitle: turbidity\nexamples:\n- value: 0.3 nephelometric turbidity units\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- turbidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000191\nalias: turbidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTrue vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).
URI: MIXS:0000397
"},{"location":"tvdss_of_hcr_press/#inheritance","title":"Inheritance","text":"name: tvdss_of_hcr_press\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original pressure was measured (e.g. 1578 m).\ntitle: depth (TVDSS) of hydrocarbon resource pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000397\nalias: tvdss_of_hcr_press\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTrue vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).
URI: MIXS:0000394
"},{"location":"tvdss_of_hcr_temp/#inheritance","title":"Inheritance","text":"name: tvdss_of_hcr_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original temperature was measured (e.g. 1345 m).\ntitle: depth (TVDSS) of hydrocarbon resource temperature\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000394\nalias: tvdss_of_hcr_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCustomary or normal density of occupants
URI: MIXS:0000771
"},{"location":"typ_occup_density/#inheritance","title":"Inheritance","text":"name: typ_occup_density\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Customary or normal density of occupants\ntitle: typical occupant density\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- typical occupant density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000771\nalias: typ_occup_density\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\nthe class_uri of the class that has been instantiated
URI: rdf:type
"},{"location":"type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no Manifest A qualified collection of DataObjects that can be analyzed together in the sa... no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no FiltrationProcess The process of segregation of phases; e no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no NamedThing a databased entity or concept/class no Configuration A set of parameters that define the actions of a process and is shared among ... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no GeneProduct A molecule encoded by a gene that has an evolved function no GenomeFeature A feature localized to an interval along a genome no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no OntologyClass A representation of class defined in an external ontology no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no Extraction A material separation in which a desired component of an input material is se... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no FailureCategorization no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no Instrument A material entity that is designed to perform a function in a scientific inve... no ProtocolExecution A PlannedProces that has PlannedProcess parts no MetagenomeSequencing Initial sequencing activity that precedes any analysis no OntologyRelation A relationship between two ontology classes as specified either directly in t... no ControlledTermValue A controlled term or class from an ontology no NomAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no LibraryPreparation no Doi A centrally registered identifier symbol used to uniquely identify objects gi... no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no TextValue A basic string value no TimestampValue A value that is a timestamp no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no QuantityValue A simple quantity, e no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no OrthologyGroup A set of genes or gene products in which all members are orthologous no MaterialEntity no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no EnvironmentalMaterialTerm no Study A study summarizes the overall goal of a research initiative and outlines the... no AttributeValue The value for any value of a attribute for a sample no PersonValue An attribute value representing a person no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no Protocol no WorkflowExecution Represents an instance of an execution of a particular workflow no DataObject An object that primarily consists of symbols that represent information no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no GeolocationValue A normalized value for a location on the earth's surface no Site no PlannedProcess no ProcessedSample no CreditAssociation This class supports binding associated researchers to studies no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetatranscriptomeAnnotation no ImageValue An attribute value representing an image no CollectingBiosamplesFromSite no Pooling physical combination of several instances of like material no PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ChemicalEntity An atom or molecule that can be represented with a chemical formula no MetabolomicsAnalysis no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no CalibrationInformation A calibration object that is associated with a process no FunctionalAnnotationAggMember no StorageProcess A planned process with the objective to preserve and protect material entitie... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no Biosample Biological source material which can be characterized by an experiment no FunctionalAnnotation An assignment of a function term (e no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no Sample A sample is a material entity that can be characterized by an experiment no MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no MetaproteomicsAnalysis no"},{"location":"type/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
name: type\ndescription: the class_uri of the class that has been instantiated\nnotes:\n- replaces legacy nmdc:type slot\n- makes it easier to read example data files\n- required for polymorphic MongoDB collections\nexamples:\n- value: nmdc:Biosample\n- value: nmdc:Study\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-schema/issues/1048\n- https://github.com/microbiomedata/nmdc-schema/issues/1233\n- https://github.com/microbiomedata/nmdc-schema/issues/248\nstructured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\nrank: 1000\nslot_uri: rdf:type\ndesignates_type: true\nalias: type\ndomain_of:\n- EukEval\n- FunctionalAnnotationAggMember\n- PeptideQuantification\n- ProteinQuantification\n- MobilePhaseSegment\n- PortionOfSubstance\n- MagBin\n- MetaboliteIdentification\n- GenomeFeature\n- FunctionalAnnotation\n- AttributeValue\n- NamedThing\n- OntologyRelation\n- FailureCategorization\n- Protocol\n- CreditAssociation\n- Doi\nrange: uriorcurie\nrequired: true\n\nSchema class definitions include structured patterns that constrain the format of their id values. One element of the structured pattern is the typecode. The following table\u2014which was derived from the schema\u2014shows which schema class can have a given string in the typecode portion of its id values.
bsm Biosample calib CalibrationInformation chcpr ChemicalConversionProcess chrcon ChromatographyConfiguration clsite CollectingBiosamplesFromSite cspro ChromatographicSeparationProcess dgms, omprc MassSpectrometry dgns, omprc NucleotideSequencing dispro DissolvingProcess dobj DataObject extrp Extraction filtpr FiltrationProcess frsite FieldResearchSite inst Instrument libprp LibraryPreparation manif Manifest mixpro MixingProcess mscon MassSpectrometryConfiguration pex ProtocolExecution poolp Pooling procsm ProcessedSample storpr StorageProcess sty Study subspr SubSamplingProcess wfmag MagsAnalysis wfmb MetabolomicsAnalysis wfmgan MetagenomeAnnotation wfmgas MetagenomeAssembly wfmp MetaproteomicsAnalysis wfmsa MetagenomeSequencing wfmtan MetatranscriptomeAnnotation wfmtas MetatranscriptomeAssembly wfmtex MetatranscriptomeExpressionAnalysis wfnom NomAnalysis wfrbt ReadBasedTaxonomyAnalysis wfrqc ReadQcAnalysis"},{"location":"unbinned_contig_num/","title":"Slot: unbinned_contig_num","text":"Number of contigs which did not end up in a medium or high quality bin.
URI: nmdc:unbinned_contig_num
"},{"location":"unbinned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"unbinned_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: unbinned_contig_num\ndescription: Number of contigs which did not end up in a medium or high quality bin.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: unbinned_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nURI: nmdc:url
"},{"location":"url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no ImageValue An attribute value representing an image no Protocol no"},{"location":"url/#properties","title":"Properties","text":"name: url\nnotes:\n- See issue 207 - this clashes with the mixs field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: url\ndomain_of:\n- ImageValue\n- Protocol\n- DataObject\nrange: string\n\ncalibration information is used by a process
URI: nmdc:uses_calibration
"},{"location":"uses_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NomAnalysis no MetabolomicsAnalysis no"},{"location":"uses_calibration/#properties","title":"Properties","text":"name: uses_calibration\ndescription: calibration information is used by a process\ncomments:\n- Retenion index calibration data generated by a gas chromatography mass spectromery\n run is used when analyzing metabolomics data\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: uses_calibration\ndomain_of:\n- MetabolomicsAnalysis\n- NomAnalysis\nrange: CalibrationInformation\nstructured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n\nThis document is a retrospective on the changes made to the NMDC Schema between major versions 10 and 11.
Motivations for the Berkeley schema development included:
OmicsProcessing with DataGeneration\".See also: https://github.com/microbiomedata/nmdc-schema/releases/tag/v11.0.0
"},{"location":"v10-vs-v11-retrospective/#conventions","title":"Conventions:","text":"This monospaced code font is used to indicate the verbatim names of elements from the schema and variables, functions, etc. in code.UpperCamelCase are schema classes unless otherwise noted.lower_snake_case are schema slots unless otherwise noted.Vehicle.MotorVehicle.PassengerCar indicates a class hierarchy. PassengerCar is_a MotorVehicle and MotorVehicle is_a Vehicle.This major refactoring increases the number of classes in the schema from 70 to 75, but decreases the number of root classes from 19 to 17 due to better organization.
You won't find any classes designated as root classes in the schema, but they can be inferred by the absence of any is_a assertions on the class. Root classes do not inherit anything from any superclass. A routine part of schema maintenance is looking for opportunities to group and generalize similar root classes.
The Selected legacy parents column is provided to highlight two groups of updates that are discussed further below. Not every parent is shown for every legacy class.
Removed legacy class New/Replacement class from Berkeley schema Selected legacy parentsActivity AnalyticalSample BiosampleProcessing BooleanValue AttributeValue IntegerValue AttributeValue MagsAnalysisActivity MagsAnalysis WorkflowExecutionActivity MetaboliteQuantification MetaboliteIdentification MetabolomicsAnalysisActivity MetabolomicsAnalysis WorkflowExecutionActivity MetagenomeAnnotationActivity MetagenomeAnnotation WorkflowExecutionActivity MetagenomeSequencingActivity MetagenomeSequencing WorkflowExecutionActivity MetaproteomicsAnalysisActivity MetaproteomicsAnalysis WorkflowExecutionActivity MetatranscriptomeAnnotationActivity MetatranscriptomeAnnotation WorkflowExecutionActivity NomAnalysisActivity NomAnalysis WorkflowExecutionActivity OmicsProcessing DataGeneration Reaction ReactionParticipant ReadBasedTaxonomyAnalysisActivity ReadBasedTaxonomyAnalysis WorkflowExecutionActivity ReadQcAnalysisActivity ReadQcAnalysis WorkflowExecutionActivity Solution SolutionComponent UrlValue AttributeValue WorkflowExecutionActivity CalibrationInformation ChemicalConversionProcess ChromatographyConfiguration Configuration DissolvingProcess InformationObject Instrument MassSpectrometry MassSpectrometryConfiguration MaterialProcessing MobilePhaseSegment NucleotideSequencing PortionOfSubstance ProtocolExecution StorageProcess WorkflowExecution For example, the MetagenomeAnnotationActivity class used to be located in the hierarchy Activity.WorkFlowExecutionActivity, but now it and 11 similar classes are located in the hierarchy NamedThing.PlannedProcess.WorkflowExecution. The word Activity, inherited from the Provenance Ontology, has largely been removed from the schema, as PlannedProcess from the Ontology of Biomedical Investigations now plays a more important organizational role.
ProtocolExecution has been added as a PlannedProcess for aggregating other processes together when they follow the same Protocol.
Several other kinds of processual classes were also migrated into the NamedThing.PlannedProcess, with or without renaming or other refactoring. For example, the fairly vague root class OmicsProcessing is now NamedThing.PlannedProcess.DataGeneration, which now has the following subclasses:
MassSpectrometryNucleotideSequencingThe legacy BiosampleProcessing class (including Pooling, LibraryPreparation) and some classes that were previously direct subclasses of PlannedProcess (Extraction, SubSamplingProcess, MixingProcess, FiltrationProcess, ChromatographicSeparationProcess) have been re-rooted into a new MaterialProcessing class.
DissolvingProcess and ChemicalConversionProcess are new subclasses of MaterialProcessing.
StorageProcess has been added as a new PlannedProcess but the schema does not classify it as a MaterialProcessing because it does not intrinsically create new/modified samples.
Terms that implied quantification like MetaboliteQuantification have been renamed to reemphasize the more fundamental activity of identifying, thus MetaboliteIdentification.
A CalibrationInformation class, a Configuration class and two Configuration subclasses (illustrated below) have been added in support of chromatographic separations and mass spectrometry analyses. These are subclasses of the new InformationObject, which has also become the parent of DataObject, which used to be a direct subclass of NamedThing.
Solution-centric modelling for laboratory processes was also replaced with substance-centric modelling.
"},{"location":"v10-vs-v11-retrospective/#removed","title":"Removed:","text":"SolutionSolutionComponentPortionOfSubstanceMobilePhaseSegmentThe Berkeley schema retains the AttributeValue hierarchy but eliminates classes like IntegerValue and UrlValue, whose only advantages over values of integer or string types were never-used provenance slots.
Classes related to metabolic reactions that a cell could carry out, based on some functionality in its genome, have been removed, due to potential confusion with reactions that an experimenter might carry out in order to make a sample suitable for analysis.
"},{"location":"v10-vs-v11-retrospective/#removed_1","title":"Removed:","text":"ReactionReactionParticipantChemicalConversionProcessA very general Instrument class was added as a subclass of MaterialEntity, but without any subclasses. Knowledge about instruments is captured directly in NMDC's MongoDB database. The instances are normalized by populating their vendor slot with a value from the InstrumentVendorEnum and by populating the model slot with a value from the InstrumentModelEnum. Mappings between these NMDC vocabularies and vocabularies from collaborators like NCBI and GOLD are saved in various repos like nmdc-schema and nmdc-runtime.
AnalyticalSample was removed from the MaterialEntity hierarchy, as NMDC does not wish to imply that certain samples could be used for analyses or that others could not be used for analyses, or even that some samples are locked into an analytical path, such that they could not be subject to any more MaterialProcessing.
The number of slots in the schema remains 872 after the Berkeley merger, although there are 44 slots that have been retired from the legacy schema and 44 that were added in the switch from v10 to v11.
Many of the slot changes can be understood by looking at the Python data migration code in nmdc_schema/migrators.
A major explanation for the slot differences is the adoption of a polymorphic (i.e., multi-shaped) model for slots in the Database class, which corresponds to polymorphic collections in the v11-compliant MongoDB database. In the legacy model, the range for each of the Database slots was intended to be one class, with no provision for class hierarchy. In the new model, the range for each slot is still specified as a single class, but each Database slot can now collect instances of that specified class, plus the instances of any subclass of the specified class.
Database","text":"extraction_setlibrary_preparation_setmags_activity_setmetabolomics_analysis_activity_setmetagenome_annotation_activity_setmetagenome_assembly_setmetagenome_sequencing_activity_setmetaproteomics_analysis_activity_setmetatranscriptome_annotation_setmetatranscriptome_assembly_setmetatranscriptome_expression_analysis_setnom_analysis_activity_setomics_processing_setplanned_process_setpooling_setread_based_taxonomy_analysis_activity_setread_qc_analysis_activity_setDatabase","text":"calibration_setchemical_entity_setchromatographic_categoryconfiguration_setdata_generation_setinstrument_setmaterial_processing_setprotocol_execution_setstorage_process_setworkflow_execution_setSo now, instances of MetaproteomicsAnalysis, MetatranscriptomeAnnotation and NomAnalysis are all collected (or aggregated) in workflow_execution_set.
These polymorphic collection are enabled by a significant modeling change in v11 of the schema: a strict requirement that, within any representation of schema-compliant data, that all instances of all classes declare their own type. Furthermore, the values in the type slot must be the class_uri of the instantiated class. That, in turn, means that all classes must now declare a class_uri and that the type slots must be associated with each class. This is enforced with the following Python tests:
Note that classes should not re-associate themselves with any slot that they inherit from a superclass. For example, the class definition for Study inherits the id slot from NamedThing, so Study doesn't include id in its slots list. This no-reasserting rule is tested with test_inherited_slots_not_reiterated.py.
Also note that the legacy v10 schema did include a type slot, but it was used very inconsistently. v10 also had a similar designated_class slot which has been retired.
The following slots were removed as a consequence of removing the Reaction class and beginning the process of deprecating the Pathway class:
chemicaldirectionhas_parthas_participantsis_balancedis_diastereoselectiveis_fully_characterizedis_stereois_transportleft_participantsright_participantssmarts_stringstoichiometrycompound and has_solution_components were removed as a consequence of removing the Solution class.
The string-typed instrument_name and used were removed due to refactoring around the new Instrument class and the instrument_used slot, which is associated with numerous PlannedProcess subclasses.
The following changes have been made to slots in the Extraction class:
extractant was replaced with substances_usedextraction_method was replaced with protocol_linkextraction_target was replaced with a multivalued slot extraction_targetsThe string-typed relevant_protocols slot has been replaced with the protocol_link slot, which uses the Protocol class as its range.
The string-typed has_raw_value has been replaced with analyte_category, which has an enumerated range. The following are the permissible values for analyte_category:
metagenomemetatranscriptomemetaproteomemetabolomelipidomenomIn keeping with the focus on identification rather that quantification, has_metabolite_quantifications has been replaced with has_metabolite_identifications and metabolite_quantified has been replaced with metabolite_identified.
alternate_emails and keywords were removed due to lack of use.
The part_of slots have been replaced in many cases with more specific slots. For example, Biosample now has an associated_studies relationship with Study.
The NMDC Schema has always imported many slots from the MIxS standard, and has generally associated them with the Biosample class. In schema v11, several of those have been de-associated with Biosample as they are arguably attributes of laboratory methods, not about samples of biological materials that are extracted from some environment.
chimera_checknucl_acid_ampnucl_acid_extpcr_condpcr_primerspool_dna_extractssamp_vol_we_dna_extseq_methseq_quality_checktarget_genetarget_subfragmentSome, but not all, of those slots were re-associated with Extraction, LibraryPreparation, or NucleotideSequencing.
has_process_parts has been added to capture the relationship between a ProtocolExecution and the Process instances that were carried out with the intention of completing a specified protocol under specified circumstances.
The following slots have been added in support of the new CalibrationInformation and Configuration modelling for MassSpectrometry. The new schema's increased use of boolean and enumerated ranges (as opposed to open-ended string ranges) is nicely illustrated by these slots.
calibration_objectcalibration_standardcalibration_targetinternal_calibrationhas_chromatography_configurationhas_mass_spectrometry_configurationThe following slots have been added, specifically on MassSpectrometryConfiguration, so that a small number of MassSpectrometryConfiguration instances can be reused to describe the following:
mass_analyzersmass_spectrometry_acquisition_strategymass_spectrum_collection_modesionization_sourcepolarity_moderesolution_categoriesThese new slots are examplars of the increased emphasis on enumeration ranges (and the avoidance of the word 'type' in slot names other than type):
analyte_categorychemical_conversion_categorychromatographic_category applicable to ChromatographyConfiguration and ChromatographicSeparationProcess ?data_categoryeluent_introduction_categoryfeature_categoryprotocol_execution_categoryThe following new slots support the change from solution-based modeling to substance-based modelling:
substance_rolesubstances_usedsubstances_volumesource_concentrationfinal_concentrationsample_state_informationThe ChemicalEntity class has been refactored for nmdc-schema v11, and is likely to undergo additional changes in later 2024 and 2025. For now, a known_as slot has been added to allow for flexibility in PortionOfSubstance and retain precision in ChemicalEntity.
extraction_targets was added to Extraction. sampled_portion was added to SubSamplingProcess and jgi_portal_analysis_project_identifiers.
The following enumerations were removed:
CompoundEnumDeviceEnumprocessing_institution_enum was renamed to ProcessingInstitutionEnum.
And the following enumerations were added:
AnalyteCategoryEnumCalibrationStandardEnumCalibrationTargetEnumChemicalConversionCategoryEnumChromatographicCategoryEnumDataCategoryEnumEluentIntroductionCategoryEnumExecutionResourceEnumIonizationSourceEnumMassAnalyzerEnumMassSpectrometryAcquisitionStrategyEnumMassSpectrumCollectionModeEnumPolarityModeEnumProcessingInstitutionEnumProtocolCategoryEnumResolutionCategoryEnumSamplePortionEnumSampleStateEnumSubstanceRoleEnumExpansions for the following prefixes were added:
v10 of the schema provided 168 example data files. v11 has increased that to 224, providing better testing coverage of the schema via the run-linkml-example phase of make test.
v11 is also more thorough in annotating abstract classes, with 11, compared to 7 in v10. That includes a new abstract annotation for AttributeValue, MaterialProcessing (which essentially replaces BiosampleProcessing) and DataGeneration (which essentially replaces OmicsProcessing).
Running the whole schema though a tool like deepdiff can be overwhelming, but extracting a single class from two versions of the schema and then deep diffing them like this can be enlightening. Note that we are not curl-ing or wget-ing the schemas from GitHub, but rather using LinkML SchemaView() to fetch the root schema file and then merge in all of its imports.
The deepdiff results are then piped through yq with the -P option to convert to YAML. yq is distributed as a snap package in some Linux distributions, and snap applications can't generally write to standard output, so we add the otherwise redundant step of piping the output though cat in order to write to a file.
pre_schema.yaml:\n poetry run python -c 'from linkml_runtime.utils.schemaview import SchemaView; \\\n from linkml_runtime.dumpers import yaml_dumper; \\\n schema_url = \"https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v10.9.1/src/schema/nmdc.yaml\"; \\\n sv = SchemaView(schema_url, merge_imports=True); \\\n yaml_dumper.dump(sv.schema, \"pre_schema.yaml\")'\n\nberkeley_schema.yaml:\n poetry run python -c 'from linkml_runtime.utils.schemaview import SchemaView; \\\n from linkml_runtime.dumpers import yaml_dumper; \\\n schema_url = \"https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v11.0.1/src/schema/nmdc.yaml\"; \\\n sv = SchemaView(schema_url, merge_imports=True); \\\n yaml_dumper.dump(sv.schema, \"berkeley_schema.yaml\")'\n\npre_study.yaml: pre_schema.yaml\n yq '.classes.Study' $< | cat > $@\n\nberkeley_study.yaml: berkeley_schema.yaml\n yq '.classes.Study' $< | cat > $@\n\npre_vs_berkeley_study.yaml: pre_study.yaml berkeley_study.yaml\n poetry run deep diff --ignore-order $^ | yq -P | cat > $@\ndictionary_item_added:\n - root['class_uri']\n - root['slot_usage']['protocol_link']\nvalues_changed:\n root['from_schema']:\n new_value: https://w3id.org/nmdc/basic_classes\n old_value: https://w3id.org/nmdc/nmdc\niterable_item_added:\n root['slots'][24]: protocol_link\niterable_item_removed:\n root['slots'][3]: id\n root['slots'][4]: alternative_identifiers\n root['slots'][9]: description\n root['slots'][26]: relevant_protocols\n root['slots'][30]: type\nThis reveals that the class_uri and protocol_link slots were added as described above. The from_schema values reveals the fact that v11 splits the elements of the schema into different YAML source files. The large number of files was intended to make it easier to debug build errors, but it has been difficult to split the contents into files that have a consistent domain or topic.
The diff also shows the removal of the id, alternative_identifiers, description, relevant_protocols and type slots, which might be counter-intuitive, until one considers that all of those slots are inherited from Study's parent, NamedThing and that schema v11 forbids re-asserting slots that are inherited from a superclass.
structured_patterns in slot_usages for approximating referential integrity, etc.","text":"LinkML slot definitions must assert their range, typically as a type (like string or float), an enumeration, or a class. If they don't, they inherit the schema's default_range, which is string in the nmdc-schema.
LinkML is able to validate that a slot, used in a data source (file or database collection), is populated with an entity of the right type (i.e. is in range) in almost all cases. Unfortunately, one of the cases that currently can not be validated is extremely important to NMDC: checking the data populated into a slot whose range is a non-inlined class. This case can also be described as the slot mentioning an instance of a class by reference. For the record, this requires that the mentioned class has an identifying slot of its own. An example of this is the associated_studies slot in the Biosample class, which has the Study class as its range. The definition of associated_studies does not assert inlined or inlined_as_list to be true, and the Study class inherits the id slot as an identifier from NamedThing. Therefore, the value of an associated_studies slot in a data file must be the id of a Study.
In the absense of any other data or constraints, the nmdc-schema will consider the following assertion valid for a Biosample, even if xyz isn't defined in the same data source:
associated_studies:\n - xyz\nIf xyz is defined in the data source and it does not pass validation as a Study, then the Biosample will also be considered invalid. Unfortunately, the definitions and mentions of nmdc-schema instances are frequently split across different MongoDB collections, so validating that a referred instance is really of the right type is non-trivial.
As a very lightweight guard against referring to instances of the wrong type, stuctured_patterns were added to slot_usages in berkeley-schema-fy24, and also independently in nmdc-schema v10 during the development of berkeley-schema-fy24/v11. In addition to being incomplete, this solution introduces some minor problems into the schema, and it relies on some other advanced LinkML features. Still, it has been useful in debugging some schema/data problems that slipped though the cracks in the past.
For example, the following can be found inside of Biosample's slot_usage block now:
associated_studies:\n required: true\n range: Study\n structured_pattern:\n syntax: \"{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$\"\n interpolated: true\nThat means that the value after associated_studies: in a Biosample must be the id of a Study instance, but also must be a string matching some pattern. The pattern is only revealed if all of the syntax elements in curly brackets are defined in the settings block of the schema, and if the schema has been fed though the gen-likml command line too with --materialize-patterns enabled. In the nmdc_schema/nmdc_materialized_patterns.yaml schema, one can see the intended pattern:
associated_studies:\n name: associated_studies\n range: Study\n required: true\n pattern: ^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\nTherefore, when using nmdc_schema/nmdc_materialized_patterns.yaml for validation, a Biosample with this assertion:
associated_studies:\n - xyz\nwould fail validation, because 'xyz' does not match '^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$' (See https://regexr.com/87a0s). NMDC's use of structured_pattern slot_usages is a manual effort to align the id pattern specified in a class's definition with a constraint on how identifiers for instances of that class are mentioned in a slot.
Now that we have addressed structured_patterns including settings and gen-linkml, let's address slot_usages, which are attributes of LinkML classes that are intended to refine the behavior of slots, relative to their global definition within the schema. For example, here's the global definition of has_input:
has_input:\n aliases:\n - input\n range: NamedThing\n multivalued: true\n description: >-\n An input to a process.\nThe only constraint is that the value of has_input must be the id of a NamedThing, since has_input doesn't assert inlined or inlined_as_list, and NamedThing used id as it's identifying slot. As previously mentioned, structured_patterns can be used to improve the validation of this slot in some circumstances, but there are multiple classes that use has_input, and they don't all use the same range for has_input. For example, CollectingBiosamplesFromSite specifies that it's range for has_input is Site. Note that not all nmdc-schema contributors are in favor of those semantics.
has_input:\n range: Site\n description: >-\n The site from which samples are collected.\nThat slot_usage does not assert a structured_pattern, but many of them do. There are also classes that use has_input without any range constraint in their slot_usage, but might be clearer if they did. For example, WorkflowExecution should probably specify that it only uses DataObject in the range of its has_input. This would provide useful clarity to diagramming tools like refgraph.
Finally, we should point out that some slot_usage ranges in nmdc-schema use the LinkML any_of construct. For example, here's part of the slot_usage for MaterialProcessing:
has_input:\n any_of:\n - range: Biosample\n - range: ProcessedSample\n structured_pattern:\n syntax: \"{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$\"\n interpolated: true\nThat might be seen as asserting that MaterialProcessing's range is either Biosample or ProcessedSample, but has_input has the global range of NamedThing, so the effective range for has_input in MaterialProcessing is the union of NamedThing, Biosample and ProcessedSample.
Note that the slot_usage strucutred_pattern essentially asserts two different strucutured_pattern syntaxes, due to the use of the | character: \"{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$\" for Biosamples and \"{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$\" for ProcessedSamples.
slot_usage is complex to understand and use.structured_pattern requires the definition of settings and pattern materialization with gen-linkml in order to be useful.id patterns in class definitions, slot_usage structured_patterns, and slot_usage ranges.any_of ranges may not match LinkML's union-based understanding.any_of ranges can easily override global slot definitions, when they are meant to refine them (in the spirit of monotonicity).slot_usage structured_patterns, as used in the nmdc-schema, imply that the ranges of some slots are both a referred thing (asserted in the range), and a string (by way of the pattern). That can never be true, and it breaks the functionality of some derived artifacts, such as OWL and RDF.The LinkML and NMDC teams are currently working on more sophisticated solutions for interpreting any_of ranges, checking referential integrity and for making structured_pattern materialization the default in any situation that used the schema.
Please see LinkML Validation documentation for general information on validation with LinkML. It has several good examples of how to use linkml-validate in a python script or from the command line. https://linkml.io/linkml/data/validating-data.html
Using the examples in src/docs/examples, we can validate the data against the schema in python:
from linkml.validator import validate\n\ninstance = {\n \"id\": \"nmdc:bsm-99-dtTMNb\",\n \"associated_studies\": [\"nmdc:study-00-abc123\"],\n \"env_broad_scale\": {\n \"has_raw_value\": \"ENVO:00002030\",\n \"term\": {\n \"id\": \"ENVO:00002030\"\n }\n },\n \"env_local_scale\": {\n \"has_raw_value\": \"ENVO:00002169\",\n \"term\": {\n \"id\": \"ENVO:00002169\"\n }\n },\n \"env_medium\": {\n \"has_raw_value\": \"ENVO:00005792\",\n \"term\": {\n \"id\": \"ENVO:00005792\"\n }\n },\n \"type\": \"nmdc:Biosample\",\n \"analysis_type\": [\n \"amplicon sequencing assay\",\n \"metagenomics\"\n ]\n}\n\nreport = validate(instance, \"nmdc.yaml\", \"Biosample\")\n\nif not report.results:\n print('The instance is valid!')\nelse:\n for result in report.results:\n print(result.message)\nURI: nmdc:value
"},{"location":"value/#properties","title":"Properties","text":"name: value\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: value\nrange: QuantityValue\n\nURI: nmdc:vendor
"},{"location":"vendor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Instrument A material entity that is designed to perform a function in a scientific inve... no"},{"location":"vendor/#properties","title":"Properties","text":"name: vendor\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: vendor\ndomain_of:\n- Instrument\nrange: InstrumentVendorEnum\n\nVentilation rate of the system in the sampled premises
URI: MIXS:0000114
"},{"location":"ventilation_rate/#inheritance","title":"Inheritance","text":"name: ventilation_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per minute, liters per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ventilation rate of the system in the sampled premises\ntitle: ventilation rate\nexamples:\n- value: 750 cubic meter per minute\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000114\nalias: ventilation_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nVentilation system used in the sampled premises
URI: MIXS:0000756
"},{"location":"ventilation_type/#inheritance","title":"Inheritance","text":"name: ventilation_type\nannotations:\n expected_value:\n tag: expected_value\n value: ventilation type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ventilation system used in the sampled premises\ntitle: ventilation type\nexamples:\n- value: Operable windows\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000756\nalias: ventilation_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:version
"},{"location":"version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NomAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MetabolomicsAnalysis no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetatranscriptomeAssembly no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no MetatranscriptomeAnnotation no MetaproteomicsAnalysis no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"version/#properties","title":"Properties","text":"name: version\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: version\ndomain_of:\n- WorkflowExecution\nrange: string\n\nConcentration of Volatile Fatty Acids in the sample
URI: MIXS:0000152
"},{"location":"vfa/#inheritance","title":"Inheritance","text":"name: vfa\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of Volatile Fatty Acids in the sample\ntitle: volatile fatty acids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile fatty acids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000152\nalias: vfa\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nOriginal volatile fatty acid concentration in the hydrocarbon resource
URI: MIXS:0000408
"},{"location":"vfa_fw/#inheritance","title":"Inheritance","text":"name: vfa_fw\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original volatile fatty acid concentration in the hydrocarbon resource\ntitle: vfa in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- vfa in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000408\nalias: vfa_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe building visual media
URI: MIXS:0000840
"},{"location":"vis_media/#inheritance","title":"Inheritance","text":"name: vis_media\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building visual media\ntitle: visual media\nexamples:\n- value: 3D scans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- visual media\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000840\nalias: vis_media\ndomain_of:\n- Biosample\nrange: vis_media_enum\nmultivalued: false\n\nA measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)
URI: MIXS:0000126
"},{"location":"viscosity/#inheritance","title":"Inheritance","text":"name: viscosity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: cP at degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\ntitle: viscosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- viscosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000126\nalias: viscosity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThis inter-collection relationship diagram shows the database collections described by the schema, and the relationships between those collections.
Each circle represents a collection. Each arrow represents all of the fields that documents in one collection\u2014the one at that arrow's tail\u2014can use to refer to documents in another collection\u2014the one at that arrow's head. If you click on a circle, the names of the fields will appear on the arrows connected to that circle.
"},{"location":"volatile_org_comp/","title":"Slot: volatile organic compounds (volatile_org_comp)","text":"Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound
URI: MIXS:0000115
"},{"location":"volatile_org_comp/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: volatile_org_comp\nannotations:\n expected_value:\n tag: expected_value\n value: volatile organic compound name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per cubic meter, parts per million, nanogram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of carbon-based chemicals that easily evaporate at room\n temperature; can report multiple volatile organic compounds by entering numeric\n values preceded by name of compound\ntitle: volatile organic compounds\nexamples:\n- value: formaldehyde;500 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile organic compounds\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000115\nalias: volatile_org_comp\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe volume of a substance.
URI: nmdc:volume
"},{"location":"volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... yes SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no FiltrationProcess The process of segregation of phases; e yes"},{"location":"volume/#properties","title":"Properties","text":"name: volume\ndescription: The volume of a substance.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: volume\ndomain_of:\n- Extraction\n- SubSamplingProcess\n- FiltrationProcess\n- MobilePhaseSegment\n- PortionOfSubstance\nrange: QuantityValue\n\nThe total area of the sampled room's walls
URI: MIXS:0000198
"},{"location":"wall_area/#inheritance","title":"Inheritance","text":"name: wall_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total area of the sampled room's walls\ntitle: wall area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000198\nalias: wall_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe building class of the wall defined by the composition of the building elements and fire-resistance rating.
URI: MIXS:0000841
"},{"location":"wall_const_type/#inheritance","title":"Inheritance","text":"name: wall_const_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building class of the wall defined by the composition of the building\n elements and fire-resistance rating.\ntitle: wall construction type\nexamples:\n- value: fire resistive\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall construction type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000841\nalias: wall_const_type\ndomain_of:\n- Biosample\nrange: wall_const_type_enum\nmultivalued: false\n\nThe material utilized to finish the outer most layer of the wall
URI: MIXS:0000842
"},{"location":"wall_finish_mat/#inheritance","title":"Inheritance","text":"name: wall_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material utilized to finish the outer most layer of the wall\ntitle: wall finish material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000842\nalias: wall_finish_mat\ndomain_of:\n- Biosample\nrange: wall_finish_mat_enum\nmultivalued: false\n\nThe average height of the walls in the sampled room
URI: MIXS:0000221
"},{"location":"wall_height/#inheritance","title":"Inheritance","text":"name: wall_height\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average height of the walls in the sampled room\ntitle: wall height\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000221\nalias: wall_height\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe relative location of the wall within the room
URI: MIXS:0000843
"},{"location":"wall_loc/#inheritance","title":"Inheritance","text":"name: wall_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the wall within the room\ntitle: wall location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000843\nalias: wall_loc\ndomain_of:\n- Biosample\nrange: wall_loc_enum\nmultivalued: false\n\nThe surface treatment of interior wall
URI: MIXS:0000845
"},{"location":"wall_surf_treatment/#inheritance","title":"Inheritance","text":"name: wall_surf_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The surface treatment of interior wall\ntitle: wall surface treatment\nexamples:\n- value: paneling\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall surface treatment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000845\nalias: wall_surf_treatment\ndomain_of:\n- Biosample\nrange: wall_surf_treatment_enum\nmultivalued: false\n\nThe feel, appearance, or consistency of a wall surface
URI: MIXS:0000846
"},{"location":"wall_texture/#inheritance","title":"Inheritance","text":"name: wall_texture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The feel, appearance, or consistency of a wall surface\ntitle: wall texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000846\nalias: wall_texture\ndomain_of:\n- Biosample\nrange: wall_texture_enum\nmultivalued: false\n\nThe ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint
URI: MIXS:0000222
"},{"location":"wall_thermal_mass/#inheritance","title":"Inheritance","text":"name: wall_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the wall to provide inertia against temperature fluctuations.\n Generally this means concrete or concrete block that is either exposed or covered\n only with paint\ntitle: wall thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000222\nalias: wall_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSigns of the presence of mold or mildew on a wall
URI: MIXS:0000844
"},{"location":"wall_water_mold/#inheritance","title":"Inheritance","text":"name: wall_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on a wall\ntitle: wall signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000844\nalias: wall_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:was_generated_by
"},{"location":"was_generated_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e yes FunctionalAnnotationAggMember yes DataObject An object that primarily consists of symbols that represent information yes"},{"location":"was_generated_by/#properties","title":"Properties","text":"name: was_generated_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasGeneratedBy\nrank: 1000\nalias: was_generated_by\ndomain_of:\n- FunctionalAnnotationAggMember\n- FunctionalAnnotation\n- DataObject\nrange: WorkflowExecution\nany_of:\n- range: WorkflowExecution\n- range: DataGeneration\n\nURI: nmdc:was_informed_by
"},{"location":"was_informed_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NomAnalysis yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes MetabolomicsAnalysis yes ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... yes MetagenomeSequencing Initial sequencing activity that precedes any analysis yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes MetatranscriptomeAssembly yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes MetatranscriptomeAnnotation yes MetaproteomicsAnalysis yes WorkflowExecution Represents an instance of an execution of a particular workflow yes"},{"location":"was_informed_by/#properties","title":"Properties","text":"name: was_informed_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nstructured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\nmappings:\n- prov:wasInformedBy\nrank: 1000\nalias: was_informed_by\ndomain_of:\n- WorkflowExecution\nrange: DataGeneration\n\nThe origin of wastewater such as human waste, rainfall, storm drains, etc.
URI: MIXS:0000353
"},{"location":"wastewater_type/#inheritance","title":"Inheritance","text":"name: wastewater_type\nannotations:\n expected_value:\n tag: expected_value\n value: wastewater type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The origin of wastewater such as human waste, rainfall, storm drains,\n etc.\ntitle: wastewater type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wastewater type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000353\nalias: wastewater_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nReference or method used in determining the water content of soil
URI: MIXS:0000323
"},{"location":"water_cont_soil_meth/#inheritance","title":"Inheritance","text":"name: water_cont_soil_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the water content of soil\ntitle: water content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000323\nalias: water_cont_soil_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nWater content measurement
URI: MIXS:0000185
"},{"location":"water_content/#inheritance","title":"Inheritance","text":"name: water_content\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water content measurement\ntitle: water content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000185\nalias: water_content\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nMeasurement of magnitude and direction of flow within a fluid
URI: MIXS:0000203
"},{"location":"water_current/#inheritance","title":"Inheritance","text":"name: water_current\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per second, knots\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of magnitude and direction of flow within a fluid\ntitle: water current\nexamples:\n- value: 10 cubic meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water current\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000203\nalias: water_current\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCurrent amount of water (%) in a produced fluid stream; or the average of the combined streams
URI: MIXS:0000454
"},{"location":"water_cut/#inheritance","title":"Inheritance","text":"name: water_cut\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Current amount of water (%) in a produced fluid stream; or the average\n of the combined streams\ntitle: water cut\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water cut\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000454\nalias: water_cut\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe size of the water feature
URI: MIXS:0000223
"},{"location":"water_feat_size/#inheritance","title":"Inheritance","text":"name: water_feat_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The size of the water feature\ntitle: water feature size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000223\nalias: water_feat_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of water feature present within the building being sampled
URI: MIXS:0000847
"},{"location":"water_feat_type/#inheritance","title":"Inheritance","text":"name: water_feat_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of water feature present within the building being sampled\ntitle: water feature type\nexamples:\n- value: stream\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000847\nalias: water_feat_type\ndomain_of:\n- Biosample\nrange: water_feat_type_enum\nmultivalued: false\n\nWater production rates per well (e.g. 987 m3 / day)
URI: MIXS:0000453
"},{"location":"water_prod_rate/#inheritance","title":"Inheritance","text":"name: water_prod_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water production rates per well (e.g. 987 m3 / day)\ntitle: water production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000453\nalias: water_prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000590
"},{"location":"water_temp_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: water_temp_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to water with varying\n degree of temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple regimens\ntitle: water temperature regimen\nexamples:\n- value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000590\nalias: water_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nInformation about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000591
"},{"location":"watering_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: watering_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milliliter, liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to watering frequencies,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can include\n multiple regimens\ntitle: watering regimen\nexamples:\n- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- watering regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000591\nalias: watering_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA list of websites that are associated with the entity.
URI: nmdc:websites
"},{"location":"websites/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
Regex pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$
name: websites\ndescription: A list of websites that are associated with the entity.\ncomments:\n- DOIs should not be included as websites. Instead, use the associated_dois slot.\n- A consortium's homepage website should be included in the homepage_website slot,\n not in websites.\n- consortium is a convenience term for a Study whose study_category value is consortium\n- the website slot and its subproperties are virtually identical to the url slot,\n except that they are multivalued and url is single-valued.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:url\nrank: 1000\nalias: websites\ndomain_of:\n- PersonValue\n- Study\nrange: string\nmultivalued: true\npattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n\nThe day of the week when sampling occurred
URI: MIXS:0000848
"},{"location":"weekday/#inheritance","title":"Inheritance","text":"name: weekday\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The day of the week when sampling occurred\ntitle: weekday\nexamples:\n- value: Sunday\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weekday\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000848\nalias: weekday\ndomain_of:\n- Biosample\nrange: weekday_enum\nmultivalued: false\n\nA unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)
URI: MIXS:0000297
"},{"location":"win/#inheritance","title":"Inheritance","text":"name: win\nannotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'A unique identifier of a well or wellbore. This is part of the Global\n Framework for Well Identification initiative which is compiled by the Professional\n Petroleum Data Management Association (PPDM) in an effort to improve well identification\n systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\ntitle: well identification number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- well identification number\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000297\nalias: win\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nWind direction is the direction from which a wind originates
URI: MIXS:0000757
"},{"location":"wind_direction/#inheritance","title":"Inheritance","text":"name: wind_direction\nannotations:\n expected_value:\n tag: expected_value\n value: wind direction name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Wind direction is the direction from which a wind originates\ntitle: wind direction\nexamples:\n- value: Northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind direction\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000757\nalias: wind_direction\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSpeed of wind measured at the time of sampling
URI: MIXS:0000118
"},{"location":"wind_speed/#inheritance","title":"Inheritance","text":"name: wind_speed\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second, kilometer per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Speed of wind measured at the time of sampling\ntitle: wind speed\nexamples:\n- value: 21 kilometer per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind speed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000118\nalias: wind_speed\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe physical condition of the window at the time of sampling
URI: MIXS:0000849
"},{"location":"window_cond/#inheritance","title":"Inheritance","text":"name: window_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the window at the time of sampling\ntitle: window condition\nexamples:\n- value: rupture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000849\nalias: window_cond\ndomain_of:\n- Biosample\nrange: window_cond_enum\nmultivalued: false\n\nThe type of window covering
URI: MIXS:0000850
"},{"location":"window_cover/#inheritance","title":"Inheritance","text":"name: window_cover\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of window covering\ntitle: window covering\nexamples:\n- value: curtains\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window covering\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000850\nalias: window_cover\ndomain_of:\n- Biosample\nrange: window_cover_enum\nmultivalued: false\n\nThe horizontal position of the window on the wall
URI: MIXS:0000851
"},{"location":"window_horiz_pos/#inheritance","title":"Inheritance","text":"name: window_horiz_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The horizontal position of the window on the wall\ntitle: window horizontal position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window horizontal position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000851\nalias: window_horiz_pos\ndomain_of:\n- Biosample\nrange: window_horiz_pos_enum\nmultivalued: false\n\nThe relative location of the window within the room
URI: MIXS:0000852
"},{"location":"window_loc/#inheritance","title":"Inheritance","text":"name: window_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the window within the room\ntitle: window location\nexamples:\n- value: west\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000852\nalias: window_loc\ndomain_of:\n- Biosample\nrange: window_loc_enum\nmultivalued: false\n\nThe type of material used to finish a window
URI: MIXS:0000853
"},{"location":"window_mat/#inheritance","title":"Inheritance","text":"name: window_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material used to finish a window\ntitle: window material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000853\nalias: window_mat\ndomain_of:\n- Biosample\nrange: window_mat_enum\nmultivalued: false\n\nThe number of times windows are opened per week
URI: MIXS:0000246
"},{"location":"window_open_freq/#inheritance","title":"Inheritance","text":"name: window_open_freq\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times windows are opened per week\ntitle: window open frequency\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window open frequency\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000246\nalias: window_open_freq\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe window's length and width
URI: MIXS:0000224
"},{"location":"window_size/#inheritance","title":"Inheritance","text":"name: window_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: inch, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The window's length and width\ntitle: window area/size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window area/size\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit} x {float} {unit}'\nslot_uri: MIXS:0000224\nalias: window_size\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDefines whether the windows were open or closed during environmental testing
URI: MIXS:0000855
"},{"location":"window_status/#inheritance","title":"Inheritance","text":"name: window_status\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Defines whether the windows were open or closed during environmental\n testing\ntitle: window status\nexamples:\n- value: open\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window status\nrank: 1000\nis_a: core field\nstring_serialization: '[closed|open]'\nslot_uri: MIXS:0000855\nalias: window_status\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe type of windows
URI: MIXS:0000856
"},{"location":"window_type/#inheritance","title":"Inheritance","text":"name: window_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of windows\ntitle: window type\nexamples:\n- value: fixed window\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000856\nalias: window_type\ndomain_of:\n- Biosample\nrange: window_type_enum\nmultivalued: false\n\nThe vertical position of the window on the wall
URI: MIXS:0000857
"},{"location":"window_vert_pos/#inheritance","title":"Inheritance","text":"name: window_vert_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The vertical position of the window on the wall\ntitle: window vertical position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window vertical position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000857\nalias: window_vert_pos\ndomain_of:\n- Biosample\nrange: window_vert_pos_enum\nmultivalued: false\n\nSigns of the presence of mold or mildew on the window.
URI: MIXS:0000854
"},{"location":"window_water_mold/#inheritance","title":"Inheritance","text":"name: window_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the window.\ntitle: window signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000854\nalias: window_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThis property links a database object to the set of workflow executions.
URI: nmdc:workflow_execution_set
"},{"location":"workflow_execution_set/#inheritance","title":"Inheritance","text":"Range: WorkflowExecution
Multivalued: True
name: workflow_execution_set\ndescription: This property links a database object to the set of workflow executions.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: workflow_execution_set\ndomain_of:\n- Database\nrange: WorkflowExecution\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of xylene in the sample
URI: MIXS:0000156
"},{"location":"xylene/#inheritance","title":"Inheritance","text":"name: xylene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of xylene in the sample\ntitle: xylene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- xylene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000156\nalias: xylene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of zinc in the sample
URI: nmdc:zinc
"},{"location":"zinc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"zinc/#properties","title":"Properties","text":"name: zinc\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of zinc in the sample\ntitle: zinc\nexamples:\n- value: 2.5 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- zinc\nrank: 1000\nalias: zinc\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe NMDC Schema is a foundational framework designed to standardize metadata for the National Microbiome Data Collaborative (NMDC) and collaborating data providors. By establishing a structured approach to metadata, the NMDC Schema enables researchers to organize, share, and interpret complex datasets with consistency and clarity. The NMDC Schema is critical substrate used to facilitate interoperability and collaboration, as it provide a common language for data exchange across systems and disciplines. In the context of the NMDC, this schema supports the integration of microbiome data from medicine, agriculture, bioenergy, and environmental science into a cohesive platform.
This schema is organized into two modules:
A core set of elements for representing data values represented in LinkML format (https://w3id.org/linkml/) consisting of a set classes, slots, types, and enumerations that are used to define the structure of the NMDC schema.
A subset of the MIxS schema developed by the Genomic Standards Consortium, that is used to describe the environmental context of samples.
URI: https://w3id.org/nmdc/nmdc
"},{"location":"#classes","title":"Classes","text":"Class Description AttributeValue The value for any value of a attribute for a sample ControlledTermValue A controlled term or class from an ontology ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... GeolocationValue A normalized value for a location on the earth's surface ImageValue An attribute value representing an image PersonValue An attribute value representing a person QuantityValue A simple quantity, e TextValue A basic string value TimestampValue A value that is a timestamp CreditAssociation This class supports binding associated researchers to studies Database An abstract holder for any set of metadata and data Doi A centrally registered identifier symbol used to uniquely identify objects gi... EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... FailureCategorization FunctionalAnnotation An assignment of a function term (e FunctionalAnnotationAggMember GenomeFeature A feature localized to an interval along a genome MagBin MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... NamedThing a databased entity or concept/class GeneProduct A molecule encoded by a gene that has an evolved function InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... CalibrationInformation A calibration object that is associated with a process Configuration A set of parameters that define the actions of a process and is shared among ... ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... DataObject An object that primarily consists of symbols that represent information Manifest A qualified collection of DataObjects that can be analyzed together in the sa... MaterialEntity Instrument A material entity that is designed to perform a function in a scientific inve... Sample A sample is a material entity that can be characterized by an experiment Biosample Biological source material which can be characterized by an experiment ProcessedSample Site FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected OntologyClass A representation of class defined in an external ontology ChemicalEntity An atom or molecule that can be represented with a chemical formula EnvironmentalMaterialTerm FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... OrthologyGroup A set of genes or gene products in which all members are orthologous Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... PlannedProcess CollectingBiosamplesFromSite DataGeneration The methods and processes used to generate omics data from a biosample or org... MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... DissolvingProcess A mixing step where a soluble component is mixed with a liquid component Extraction A material separation in which a desired component of an input material is se... FiltrationProcess The process of segregation of phases; e LibraryPreparation MixingProcess The combining of components, particles or layers into a more homogeneous stat... Pooling physical combination of several instances of like material SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... ProtocolExecution A PlannedProces that has PlannedProcess parts StorageProcess A planned process with the objective to preserve and protect material entitie... WorkflowExecution Represents an instance of an execution of a particular workflow MagsAnalysis A workflow execution activity that uses computational binning tools to group ... MetabolomicsAnalysis MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... MetagenomeSequencing Initial sequencing activity that precedes any analysis MetaproteomicsAnalysis MetatranscriptomeAnnotation MetatranscriptomeAssembly MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... NomAnalysis ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... Study A study summarizes the overall goal of a research initiative and outlines the... OntologyRelation A relationship between two ontology classes as specified either directly in t... PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein Protocol"},{"location":"#slots","title":"Slots","text":"Slot Description abs_air_humidity Actual mass of water vapor - mh20 - present in the air water vapor mixture add_date The date on which the information was added to the database add_recov_method Additional (i additional_info Information that doesn't fit anywhere else address The street name and building number where the sampling occurred adj_room List of rooms (room number, room name) immediately adjacent to the sampling r... aero_struc Aerospace structures typically consist of thin plates with stiffeners for the... agrochem_addition Addition of fertilizers, pesticides, etc air_PM_concen Concentration of substances that remain suspended in the air, and comprise mi... air_temp Temperature of the air at the time of sampling air_temp_regm Information about treatment involving an exposure to varying temperatures; sh... al_sat Aluminum saturation (esp al_sat_meth Reference or method used in determining Al saturation alkalinity Alkalinity, the ability of a solution to neutralize acids to the equivalence ... alkalinity_method Method used for alkalinity measurement alkyl_diethers Concentration of alkyl diethers all_proteins the list of protein identifiers that are associated with the peptide sequence alt Altitude is a term used to identify heights of objects such as airplanes, spa... alternative_descriptions A list of alternative descriptions for the entity alternative_identifiers A list of alternative identifiers for the entity alternative_names A list of alternative names used to refer to the entity alternative_titles A list of alternative titles for the entity aminopept_act Measurement of aminopeptidase activity ammonium Concentration of ammonium in the sample ammonium_nitrogen Concentration of ammonium nitrogen in the sample amount_light The unit of illuminance and luminous emittance, measuring luminous flux per u... analysis_identifiers analysis_type Select all the data types associated or available for this biosample analyte_category The type of analyte(s) that were measured in the data generation process and ... ances_data Information about either pedigree or other ancestral information description ... annual_precpt The average of all annual precipitation values known, or an estimated equival... annual_temp Mean annual temperature antibiotic_regm Information about treatment involving antibiotic administration; should inclu... api API gravity is a measure of how heavy or light a petroleum liquid is compared... applied_roles applies_to_person arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c... aromatics_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... asm_score A score for comparing metagenomic assembly quality from same sample asphaltenes_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... assembly_identifiers associated_dois A list of DOIs associated with a resource, such as a list of DOIS associated ... associated_studies The study associated with a resource atmospheric_data Measurement of atmospheric data; can include multiple data avg_dew_point The average of dew point measures taken at the beginning of every hour over a... avg_occup Daily average occupancy of room avg_temp The average of temperatures taken at the beginning of every hour over a 24 ho... bac_prod Bacterial production in the water column measured by isotope uptake bac_resp Measurement of bacterial respiration in the water column bacteria_carb_prod Measurement of bacterial carbon production barometric_press Force per unit area exerted against a surface by the weight of air above that... basin Name of the basin (e bathroom_count The number of bathrooms in the building bedroom_count The number of bedrooms in the building benzene Concentration of benzene in the sample best_protein the specific protein identifier most correctly associated with the peptide se... bin_name Name of the metagenome-assembled genome bin_quality The quality of the metagenome-assembled genome based on MIMAG standards (http... binned_contig_num Number of contigs that ended up in a medium or high quality bin biochem_oxygen_dem Amount of dissolved oxygen needed by aerobic biological organisms in a body o... biocide List of biocides (commercial name of product and supplier) and date of admini... biocide_admin_method Method of biocide administration (dose, frequency, duration, time elapsed bet... biogas_retention_time biogas_temperature biol_stat The level of genome modification biomass Amount of biomass; should include the name for the part of biomass measured, ... biomaterial_purity biosample_categories biosample_identifiers biosample_set This property links a database object to the set of samples within it biotic_regm Information about treatment(s) involving use of biotic factors, such as bacte... biotic_relationship Description of relationship(s) between the subject organism and other organis... bishomohopanol Concentration of bishomohopanol blood_press_diast Resting diastolic blood pressure, measured as mm mercury blood_press_syst Resting systolic blood pressure, measured as mm mercury bromide Concentration of bromide build_docs The building design, construction and operation documents build_occup_type The primary function for which a building or discrete part of a building is i... building_setting A location (geography) where a building is set built_struc_age The age of the built structure since construction built_struc_set The characterization of the location of the built structure as high or low hu... built_struc_type A physical structure that is a body or assemblage of bodies in space to form ... bulk_elect_conductivity Electrical conductivity is a measure of the ability to carry electric current... calcium Concentration of calcium in the sample calibration_object the file containing calibration data object calibration_set This property links a database object to the set of calibrations within it calibration_standard the reference standard(s) used for calibration calibration_target the target measurement of the calibration carb_dioxide Carbon dioxide (gas) amount or concentration at the time of sampling carb_monoxide Carbon monoxide (gas) amount or concentration at the time of sampling carb_nitro_ratio Ratio of amount or concentrations of carbon to nitrogen ceil_area The area of the ceiling space within the room ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide... ceil_finish_mat The type of material used to finish a ceiling ceil_struc The construction format of the ceiling ceil_texture The feel, appearance, or consistency of a ceiling surface ceil_thermal_mass The ability of the ceiling to provide inertia against temperature fluctuation... ceil_type The type of ceiling according to the ceiling's appearance or construction ceil_water_mold Signs of the presence of mold or mildew on the ceiling chem_administration List of chemical compounds administered to the host or site where sampling oc... chem_mutagen Treatment involving use of mutagens; should include the name of mutagen, amou... chem_oxygen_dem A measure of the capacity of water to consume oxygen during the decomposition... chem_treat_method Method of chemical administration(dose, frequency, duration, time elapsed bet... chem_treatment List of chemical compounds administered upstream the sampling location where ... chemical_conversion_category The type of chemical conversion process chemical_entity_set This property links a database object to the set of chemical entities within ... chemical_formula A generic grouping for molecular formulae and empirical formulae chimera_check Tool(s) used for chimera checking, including version number and parameters, t... chloride Concentration of chloride in the sample chlorophyll Concentration of chlorophyll chromatographic_category The type of chromatography used in a process climate_environment Treatment involving an exposure to a particular climate; treatment regimen in... collected_from The Site from which a Biosample was collected collecting_biosamples_from_site_set collection_date The time of sampling, either as an instance (single point in time) or interva... collection_date_inc Date the incubation was harvested/collected/ended collection_time The time of sampling, either as an instance (single point) or interval collection_time_inc Time the incubation was harvested/collected/ended community completeness Estimate of the completeness of the metagenome-assembled genome, estimated by... completion_date compression_type If provided, specifies the compression type concentration The concentration of a substance used in a process conditionings Preliminary treatment of either phase with a suitable solution of the other p... conduc Electrical conductivity of water configuration_set This property links a database object to the set of configurations within it contained_in A type of container container_size The volume of the container an analyte is stored in or an activity takes plac... contamination Estimate of the completeness of the metagenome-assembled genome, estimated by... contig_bp Total size in bp of all contigs contigs The sum of the (length*log(length)) of all contigs, times some constant cool_syst_id The cooling system identifier core_field basic fields count crop_rotation Whether or not crop is rotated, and if yes, rotation schedule ctg_l50 Given a set of contigs, the L50 is defined as the sequence length of the shor... ctg_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... ctg_logsum Maximum contig length ctg_max Maximum contig length ctg_n50 Given a set of contigs, each with its own length, the N50 count is defined as... ctg_n90 Given a set of contigs, each with its own length, the N90 count is defined as... ctg_powsum Powersum of all contigs is the same as logsum except that it uses the sum of ... cult_root_med Name or reference for the hydroponic or in vitro culture rooting medium; can ... cur_land_use Present state of sample site cur_vegetation Vegetation classification from one or more standard classification systems, o... cur_vegetation_meth Reference or method used in vegetation classification data_category The category of the file, such as instrument data from data generation or pro... data_generation_set This property links a database object to the set of data generations within i... data_object_set This property links a database object to the set of data objects within it data_object_type The type of file represented by the data object date_created from database class date_last_rain The date of the last time it rained definition The definition of the ontology term as provided by the ontology density Density of the sample, which is its mass per unit volume (aka volumetric mass... depos_env Main depositional environment (https://en depth The vertical distance below local surface, e description a human-readable description of a thing dew_point The temperature to which a given parcel of humid air must be cooled, at const... diether_lipids Concentration of diether lipids; can include multiple types of diether lipids display_order When rendering information, this attribute to specify the order in which the ... diss_carb_dioxide Concentration of dissolved carbon dioxide in the sample or liquid portion of ... diss_hydrogen Concentration of dissolved hydrogen diss_inorg_carb Dissolved inorganic carbon concentration in the sample, typically measured af... diss_inorg_nitro Concentration of dissolved inorganic nitrogen diss_inorg_phosp Concentration of dissolved inorganic phosphorus in the sample diss_iron Concentration of dissolved iron in the sample diss_org_carb Concentration of dissolved organic carbon in the sample, liquid portion of th... diss_org_nitro Dissolved organic nitrogen concentration measured as; total dissolved nitroge... diss_oxygen Concentration of dissolved oxygen diss_oxygen_fluid Concentration of dissolved oxygen in the oil field produced fluids as it cont... dna_absorb1 260/280 measurement of DNA sample purity dna_absorb2 260/230 measurement of DNA sample purity dna_collect_site Provide information on the site your DNA sample was collected from dna_concentration dna_cont_type Tube or plate (96-well) dna_cont_well dna_container_id dna_dnase dna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA dna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... dna_project_contact dna_samp_id dna_sample_format Solution in which the DNA sample has been suspended dna_sample_name Give the DNA sample a name that is meaningful to you dna_seq_project dna_seq_project_name dna_seq_project_pi dna_volume dnase_rna doi_category The resource type the corresponding doi resolves to doi_provider The authority, or organization, the DOI is associated with doi_value A digital object identifier, which is intended to persistantly identify some ... door_comp_type The composite type of the door door_cond The phsical condition of the door door_direct The direction the door opens door_loc The relative location of the door in the room door_mat The material the door is composed of door_move The type of movement of the door door_size The size of the door door_type The type of door material door_type_metal The type of metal door door_type_wood The type of wood door door_water_mold Signs of the presence of mold or mildew on a door down_par Visible waveband radiance and irradiance measurements in the water column drainage_class Drainage classification from a standard system such as the USDA system drawings The buildings architectural drawings; if design is chosen, indicate phase-con... duration The elapsed time of an activity ecosystem An ecosystem is a combination of a physical environment (abiotic factors) and... ecosystem_category Ecosystem categories represent divisions within the ecosystem based on specif... ecosystem_path_id A unique id representing the GOLD classifiers associated with a sample ecosystem_subtype Ecosystem subtypes represent further subdivision of Ecosystem types into more... ecosystem_type Ecosystem types represent things having common characteristics within the Eco... efficiency_percent Percentage of volatile solids removed from the anaerobic digestor elev Elevation of the sampling site is its height above a fixed reference point, m... elevator The number of elevators within the built structure eluent_introduction_category A high-level categorization for how the processed sample is introduced into a... email An email address for an entity such as a person embargoed If true, the data are embargoed and not available for public access emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database emsl_identifiers emsl_project_identifiers Identifiers that link a NMDC study to the EMSL user facility website hosting ... emsl_store_temp The temperature at which the sample should be stored upon delivery to EMSL emulsions Amount or concentration of substances such as paints, adhesives, mayonnaise, ... encodes The gene product encoded by this feature end The end of the feature in positive 1-based integer coordinates end_date The date on which any process or activity was ended ended_at_time env_broad_scale Report the major environmental system the sample or specimen came from env_local_scale Report the entity or entities which are in the sample or specimen\u2019s local vic... env_medium Report the environmental material(s) immediately surrounding the sample or sp... env_package MIxS extension for reporting of measurements and observations obtained from o... environment_field field describing environmental aspect of a sample escalator The number of escalators within the built structure ethylbenzene Concentration of ethylbenzene in the sample etl_software_version from database class eukaryotic_evaluation Contains results from evaluating if a Metagenome-Assembled Genome is of eukar... execution_resource The computing resource or facility where the workflow was executed exp_duct The amount of exposed ductwork in the room exp_pipe The number of exposed pipes in the room experimental_factor Experimental factors are essentially the variable aspects of an experiment de... experimental_factor_other Other details about your sample that you feel can't be accurately represented... ext_door The number of exterior doors in the built structure ext_wall_orient The orientation of the exterior wall ext_window_orient The compass direction the exterior window of the room is facing external_database_identifiers Link to corresponding identifier in external database extraction_targets Provides the target biomolecule that has been separated from a sample during ... extreme_event Unusual physical events that may have affected microbial populations fao_class Soil classification from the FAO World Reference Database for Soil Resources feature_category A Sequence Ontology term that describes the category of a feature feature_type TODO: Yuri to write fertilizer_regm Information about treatment involving the use of fertilizers; should include ... field Name of the hydrocarbon field (e field_research_site_set file_size_bytes Size of the file in bytes filter_material A porous material on which solid particles present in air or other fluid whic... filter_method Type of filter used or how the sample was filtered filter_pore_size A quantitative or qualitative measurement of the physical dimensions of the p... filter_type A device which removes solid particulates or airborne molecular contaminants filtration_category The type of conditioning applied to a filter, device, etc final_concentration When solutions A (containing substance X) and B are combined together, this s... fire Historical and/or physical evidence of fire fireplace_type A firebox with chimney flooding Historical and/or physical evidence of flooding floor_age The time period since installment of the carpet or flooring floor_area The area of the floor space within the room floor_cond The physical condition of the floor at the time of sampling; photos or video ... floor_count The number of floors in the building, including basements and mechanical pent... floor_finish_mat The floor covering type; the finished surface that is walked on floor_struc Refers to the structural elements and subfloor upon which the finish flooring... floor_thermal_mass The ability of the floor to provide inertia against temperature fluctuations floor_water_mold Signs of the presence of mold or mildew in a room fluor Raw or converted fluorescence of water freq_clean The number of times the sample location is cleaned freq_cook The number of times a meal is cooked per week functional_annotation_agg functional_annotation_set This property links a database object to the set of all functional annotation... funding_sources A list of organizations, along with the award numbers, that underwrite financ... fungicide_regm Information about treatment involving use of fungicides; should include the n... furniture The types of furniture present in the sampled room gap_pct The gap size percentage of all scaffolds gaseous_environment Use of conditions with differing gaseous environments; should include the nam... gaseous_substances Amount or concentration of substances such as hydrogen sulfide, carbon dioxid... gc_avg Average of GC content of all contigs gc_std Standard deviation of GC content of all contigs gender_restroom The gender type of the restroom gene_count Number of genes gene_function_id The identifier for the gene function generates_calibration calibration information is generated a process genetic_mod Genetic modifications of the genome of an organism, which may occur naturally... genome_feature_set This property links a database object to the set of all features geo_loc_name The geographical origin of the sample as defined by the country or sea name f... gff_coordinate A positive 1-based integer coordinate indicating start or end git_url The url that points to the exact github location of a workflow glucosidase_act Measurement of glucosidase activity gnps_identifiers gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... gold_analysis_project_identifiers identifiers for corresponding analysis projects in GOLD gold_biosample_identifiers identifiers for corresponding sample in GOLD gold_identifiers gold_path_field This is a grouping for any of the gold path fields gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD gold_study_identifiers identifiers for corresponding project(s) in GOLD gravidity Whether or not subject is gravid, and if yes date due or date post-conception... gravity Information about treatment involving use of gravity factor to study various ... growth_facil Type of facility where the sampled plant was grown; controlled vocabulary: gr... growth_habit Characteristic shape, appearance or growth form of a plant species growth_hormone_regm Information about treatment involving use of growth hormones; should include ... gtdbtk_class Taxonomic class assigned by GTDB-Tk gtdbtk_domain Taxonomic domain assigned by GTDB-Tk gtdbtk_family Taxonomic family assigned by GTDB-Tk gtdbtk_genus Taxonomic genus assigned by GTDB-Tk gtdbtk_order Taxonomic order assigned by GTDB-Tk gtdbtk_phylum Taxonomic phylum assigned by GTDB-Tk gtdbtk_species Taxonomic genus assigned by GTDB-Tk habitat hall_count The total count of hallways and cooridors in the built structure handidness The handidness of the individual sampled has_boolean_value Links a quantity value to a boolean has_chromatography_configuration The identifier of the associated ChromatographyConfiguration, providing infor... has_credit_associations This slot links a study to a credit association has_failure_categorization has_function has_input An input to a process has_mass_spectrometry_configuration The identifier of the associated MassSpectrometryConfiguration has_maximum_numeric_value The maximum value part, expressed as number, of the quantity value when the v... has_metabolite_identifications has_minimum_numeric_value The minimum value part, expressed as number, of the quantity value when the v... has_numeric_value Links a quantity value to a number has_output An output from a process has_peptide_quantifications has_process_parts A list of process parts that make up a protocol has_raw_value The value that was specified for an annotation in raw form, i has_unit Links a QuantityValue to a unit hc_produced Main hydrocarbon type produced from resource (i hcr Main Hydrocarbon Resource type hcr_fw_salinity Original formation water salinity (prior to secondary recovery e hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en hcr_pressure Original pressure of the hydrocarbon resource hcr_temp Original temperature of the hydrocarbon resource heat_cool_type Methods of conditioning or heating a room or building heat_deliv_loc The location of heat delivery within the room heat_sys_deliv_meth The method by which the heat is delivered through the system heat_system_id The heating system identifier heavy_metals Heavy metals present in the sequenced sample and their concentrations heavy_metals_meth Reference or method used in determining heavy metals height_carper_fiber The average carpet fiber height in the indoor environment herbicide_regm Information about treatment involving use of herbicides; information about tr... highest_similarity_score homepage_website The website address (URL) of an entity's homepage horizon_meth Reference or method used in determining the horizon host_age Age of host at the time of sampling; relevant scale depends on species and st... host_body_habitat Original body habitat where the sample was obtained from host_body_product Substance produced by the body, e host_body_site Name of body site where the sample was obtained from, such as a specific orga... host_body_temp Core body temperature of the host when sample was collected host_color The color of host host_common_name Common name of the host host_diet Type of diet depending on the host, for animals omnivore, herbivore etc host_disease_stat List of diseases with which the host has been diagnosed; can include multiple... host_dry_mass Measurement of dry mass host_family_relation Familial relationships to other hosts in the same study; can include multiple... host_genotype Observed genotype host_growth_cond Literature reference giving growth conditions of the host host_height The height of subject host_last_meal Content of last meal and time since feeding; can include multiple values host_length The length of subject host_life_stage Description of life stage of host host_name host_phenotype Phenotype of human or other host host_sex Gender or physical sex of the host host_shape Morphological shape of host host_subject_id A unique identifier by which each subject can be referred to, de-identified host_subspecf_genlin Information about the genetic distinctness of the host organism below the sub... host_substrate The growth substrate of the host host_symbiont The taxonomic name of the organism(s) found living in mutualistic, commensali... host_taxid NCBI taxon id of the host, e host_tot_mass Total mass of the host at collection, the unit depends on host host_wet_mass Measurement of wet mass humidity Amount of water vapour in the air, at the time of sampling humidity_regm Information about treatment involving an exposure to varying degree of humidi... id A unique identifier for a thing igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database igsn_identifiers img_identifiers A list of identifiers that relate the biosample to records in the IMG databas... in_manifest one or more combinations of other DataObjects that can be analyzed together inchi inchi_key indoor_space A distinguishable space within a structure, the purpose for which discrete ar... indoor_surf Type of indoor surface indust_eff_percent Percentage of industrial effluents received by wastewater treatment plant infiltrations The amount of time it takes to complete each infiltration activity inorg_particles Concentration of particles such as sand, grit, metal particles, ceramics, etc input_base_count The nucleotide base count number of input reads for QC analysis input_contig_num Total number of input contigs input_mass Total mass of sample used in activity input_read_bases TODO input_read_count The sequence count number of input reads for QC analysis input_volume The volume of the input sample insdc_analysis_identifiers insdc_assembly_identifiers insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject insdc_biosample_identifiers identifiers for corresponding sample in INSDC insdc_experiment_identifiers insdc_identifiers Any identifier covered by the International Nucleotide Sequence Database Coll... insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA inside_lux The recorded value at sampling time (power density) instrument_set This property links a database object to the set of instruments within it instrument_used What instrument was used during DataGeneration or MaterialProcessing int_wall_cond The physical condition of the wall at the time of sampling; photos or video p... internal_calibration whether internal calibration was used, if false, external calibration was use... investigation_field field describing aspect of the investigation/study to which the sample belong... ionization_source The ionization source used to introduce processed samples into a mass spectro... is_pressurized Whether or not pressure was applied to a thing or process is_stranded Is the (RNA) library stranded or non-stranded (unstranded) isotope_exposure List isotope exposure or addition applied to your sample iw_bt_date_well Injection water breakthrough date per well following a secondary and/or terti... iwf Proportion of the produced fluids derived from injected water at the time of ... jgi_portal_analysis_project_identifiers identifiers for corresponding analysis projects in JGI Portal jgi_portal_identifiers identifiers for entities according to JGI Portal jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... known_as The substance from which a portion was taken language Should use ISO 639-1 code e last_clean The last time the floor was cleaned (swept, mopped, vacuumed) lat_lon The geographical origin of the sample as defined by latitude and longitude latitude latitude lbc_thirty lime buffer capacity, determined after 30 minute incubation lbceq lime buffer capacity, determined at equilibrium after 5 day incubation library_preparation_kit library_type light_intensity Measurement of light intensity light_regm Information about treatment(s) involving exposure to light, including both li... light_type Application of light to achieve some practical or aesthetic effect link_addit_analys Link to additional analysis results performed on the sample link_class_info Link to digitized soil maps or other soil classification information link_climate_info Link to climate resource lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki local_class Soil classification based on local soil classification system local_class_meth Reference or method used in determining the local soil classification location longitude longitude low_depth_contig_num Number of contigs which were excluded from binning for depth of coverage magnesium Concentration of magnesium in the sample mags_list Contains detailed information about each metagenome-assembled genome manganese Concentration of manganese in the sample manifest_category The type of context in which the constituent DataObjects can be analyzed toge... manifest_set This property links a database object to the set of manifests within it mass A physical quality that inheres in a bearer by virtue of the proportion of th... mass_analyzers The kind of mass analyzer(s) used during the spectra collection mass_spectrometry_acquisition_strategy Mode of running a mass spectrometer method by which m/z ranges are selected a... mass_spectrum_collection_modes Indicates whether mass spectra were collected in full profile, reduced profil... material_component_separation A material processing in which components of an input material become segrega... material_processing_set This property links a database object to the set of material processing withi... max_occup The maximum amount of people allowed in the indoor environment md5_checksum MD5 checksum of file (pre-compressed) mean_frict_vel Measurement of mean friction velocity mean_peak_frict_vel Measurement of mean peak friction velocity mech_struc mechanical structure: a moving structure mechanical_damage Information about any mechanical damage exerted on the plant; can include mul... members_id Names of the contigs that make up a metagenome-assembled genome metabolite_identified the specific metabolite identifier metagenome_annotation_id The identifier for the analysis activity that generated the functional annota... metagenome_assembly_parameter metaproteomics_analysis_category The category of metaproteomics analysis being performed methane Methane (gas) amount or concentration at the time of sampling mgnify_analysis_identifiers mgnify_identifiers mgnify_project_identifiers identifiers for corresponding project in MGnify micro_biomass_c_meth Reference or method used in determining microbial biomass carbon micro_biomass_meth Reference or method used in determining microbial biomass micro_biomass_n_meth Reference or method used in determining microbial biomass nitrogen microbial_biomass The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_c The part of the organic matter in the soil that constitutes living microorgan... microbial_biomass_n The part of the organic matter in the soil that constitutes living microorgan... min_q_value smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... mineral_nutr_regm Information about treatment involving the use of mineral supplements; should ... misc_param Any other measurement performed or parameter collected, that is not listed he... mod_date The last date on which the database information was modified model modifier_substance The type of modification being done n_alkanes Concentration of n-alkanes; can include multiple n-alkanes name A human readable label for an entity ncbi_lineage Comma delimited ordered list of NCBI taxonomy names ncbi_lineage_tax_ids Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId) ncbi_project_name ncbi_taxonomy_name neon_biosample_identifiers neon_identifiers identifiers for entities according to NEON neon_study_identifiers nitrate Concentration of nitrate in the sample nitrate_nitrogen Concentration of nitrate nitrogen in the sample nitrite Concentration of nitrite in the sample nitrite_nitrogen Concentration of nitrite nitrogen in the sample nitro Concentration of nitrogen (total) non_microb_biomass Amount of biomass; should include the name for the part of biomass measured, ... non_microb_biomass_method Reference or method used in determining biomass non_min_nutr_regm Information about treatment involving the exposure of plant to non-mineral nu... notes nucl_acid_amp A link to a literature reference, electronic resource or a standard operating... nucl_acid_ext A link to a literature reference, electronic resource or a standard operating... nucleic_acid_sequence_source_field num_16s Number of 16s sequences detected, a subunit of prokaryotic ribosomes num_23s Number of 23 seqeuences detected, a subunit of ribosomes num_5s Number of 5s seqeuences detected, a subunit of ribosomes num_aligned_reads The sequence count number of input reads aligned to assembled contigs num_input_reads The sequence count number of input reads for assembly num_t_rna Number of transfer transfer RNAs number_of_contig Number of contigs number_pets The number of pets residing in the sampled space number_plants The number of plant(s) in the sampling space number_resident The number of individuals currently occupying in the sampling location object object_set Applies to a property that links a database object to a set of objects objective The scientific objectives associated with the entity occup_density_samp Average number of occupants at time of sampling per square footage occup_document The type of documentation of occupancy occup_samp Number of occupants present at time of sample within the given space omics_processing_identifiers omics_type The type of omics data ontology_class_set This property links a database object to the set of ontology classes within i... orcid The ORCID of a person ordered_mobile_phases The solution(s) that moves through a chromatography column org_carb Concentration of organic carbon org_count_qpcr_info If qpcr was used for the cell count, the target gene name, the primer sequenc... org_matter Concentration of organic matter org_nitro Concentration of organic nitrogen org_nitro_method Method used for obtaining organic nitrogen org_particles Concentration of particles such as faeces, hairs, food, vomit, paper fibers, ... organism_count Total cell count of any organism (or group of organisms) per gram, volume or ... other_treatment Other treatments applied to your samples that are not applicable to the provi... output_base_count After QC analysis nucleotide base count number output_read_bases TODO output_read_count After QC analysis sequence count number owc_tvdss Depth of the original oil water contact (OWC) zone (average) (m TVDSS) oxy_stat_samp Oxygenation status of sample oxygen Oxygen (gas) amount or concentration at the time of sampling part_of Links a resource to another resource that either logically or physically incl... part_org_carb Concentration of particulate organic carbon part_org_nitro Concentration of particulate organic nitrogen particle_class Particles are classified, based on their size, into six general categories:cl... pcr_cond Description of reaction conditions and components of PCR in the form of 'init... pcr_cycles pcr_primers PCR primers that were used to amplify the sequence of the targeted gene, locu... peptide_sequence peptide_sequence_count count of peptide sequences grouped to the best_protein peptide_spectral_count sum of filter passing MS2 spectra associated with the peptide sequence within... peptide_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... permeability Measure of the ability of a hydrocarbon resource to allow fluids to pass thro... perturbation Type of perturbation, e pesticide_regm Information about treatment involving use of insecticides; should include the... petroleum_hydrocarb Concentration of petroleum hydrocarbon ph Ph measurement of the sample, or liquid portion of sample, or aqueous phase o... ph_meth Reference or method used in determining ph ph_regm Information about treatment involving exposure of plants to varying levels of... phaeopigments Concentration of phaeopigments; can include multiple phaeopigments phase The phase for a coding sequence entity phosphate Concentration of phosphate phosplipid_fatt_acid Concentration of phospholipid fatty acids; can include multiple values photon_flux Measurement of photon flux plant_growth_med Specification of the media for growing the plants or tissue cultured samples,... plant_product Substance produced by the plant, where the sample was obtained from plant_sex Sex of the reproductive parts on the whole plant, e plant_struc Name of plant structure the sample was obtained from; for Plant Ontology (PO)... polarity_mode the polarity of which ions are generated and detected pollutants Pollutant types and, amount or concentrations measured at the time of samplin... pool_dna_extracts Indicate whether multiple DNA extractions were mixed porosity Porosity of deposited sediment is volume of voids divided by the total volume... potassium Concentration of potassium in the sample pour_point Temperature at which a liquid becomes semi solid and loses its flow character... pre_treatment The process of pre-treatment removes materials that can be easily collected f... predicate pres_animal_insect The type and number of animals or insects present in the sampling space pressure Pressure to which the sample is subject to, in atmospheres prev_land_use_meth Reference or method used in determining previous land use and dates previous_land_use Previous land use and dates primary_prod Measurement of primary production, generally measured as isotope uptake primary_treatment The process to produce both a generally homogeneous liquid capable of being t... principal_investigator Principal Investigator who led the study and/or generated the dataset processed_sample_set This property links a database object to the set of processed samples within ... processing_institution The organization that processed the sample prod_rate Oil and/or gas production rates per well (e prod_start_date Date of field's first production profile_image_url A url that points to an image of a person profile_position Cross-sectional position in the hillslope where sample was collected project_id Proposal IDs or names associated with dataset proport_woa_temperature proposal_dna proposal_rna protein_spectral_count sum of filter passing MS2 spectra associated with the best protein within a g... protein_sum_masic_abundance combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... protocol_execution_category protocol_execution_set This property links a database object to the set of protocol executions withi... protocol_link qc_comment Slot to store additional comments about laboratory or workflow output qc_failure_what Provides a summary about what caused a lab or workflow process to fail qc_failure_where Describes the nmdc schema class that corresonds to where the failure occurred qc_status Stores information about the result of a process (ie the process of sequencin... quad_pos The quadrant position of the sampling room within the building radiation_regm Information about treatment involving exposure of plant or a plant part to a ... rainfall_regm Information about treatment involving an exposure to a given amount of rainfa... reactor_type Anaerobic digesters can be designed and engineered to operate using a number ... read_qc_analysis_statistic redox_potential Redox potential, measured relative to a hydrogen cell, indicating oxidation o... rel_air_humidity Partial vapor and air pressure, density of the vapor and air, or by the actua... rel_humidity_out The recorded outside relative humidity value at the time of sampling rel_samp_loc The sampling location within the train car related_identifiers Identifiers assigned to a thing that is similar to that which is represented ... relations replicate_number If sending biological replicates, indicate the rep number here reservoir Name of the reservoir (e resins_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... resolution_categories The relative resolution at which spectra were collected rna_absorb1 260/280 measurement of RNA sample purity rna_absorb2 260/230 measurement of RNA sample purity rna_collect_site Provide information on the site your RNA sample was collected from rna_concentration rna_cont_type Tube or plate (96-well) rna_cont_well rna_container_id rna_isolate_meth Describe the method/protocol/kit used to extract DNA/RNA rna_organisms List any organisms known or suspected to grow in co-culture, as well as estim... rna_project_contact rna_samp_id rna_sample_format Solution in which the RNA sample has been suspended rna_sample_name Give the RNA sample a name that is meaningful to you rna_seq_project rna_seq_project_name rna_seq_project_pi rna_volume room_air_exch_rate The rate at which outside air replaces indoor air in a given space room_architec_elem The unique details and component parts that, together, form the architecture ... room_condt The condition of the room at the time of sampling room_connected List of rooms connected to the sampling room by a doorway room_count The total count of rooms in the built structure including all room types room_dim The length, width and height of sampling room room_door_dist Distance between doors (meters) in the hallway between the sampling room and ... room_door_share List of room(s) (room number, room name) sharing a door with the sampling roo... room_hallway List of room(s) (room number, room name) located in the same hallway as sampl... room_loc The position of the room within the building room_moist_dam_hist The history of moisture damage or mold in the past 12 months room_net_area The net floor area of sampling room room_occup Count of room occupancy at time of sampling room_samp_pos The horizontal sampling position in the room relative to architectural elemen... room_type The main purpose or activity of the sampling room room_vol Volume of sampling room room_wall_share List of room(s) (room number, room name) sharing a wall with the sampling roo... room_window_count Number of windows in the room root_cond Relevant rooting conditions such as field plot size, sowing density, containe... root_med_carbon Source of organic carbon in the culture rooting medium; e root_med_macronutr Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... root_med_micronutr Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, ... root_med_ph pH measurement of the culture rooting medium; e root_med_regl Growth regulators in the culture rooting medium such as cytokinins, auxins, g... root_med_solid Specification of the solidifying agent in the culture rooting medium; e root_med_suppl Organic supplements of the culture rooting medium, such as vitamins, amino ac... salinity The total concentration of all dissolved salts in a liquid or solid sample salinity_category Categorical description of the sample's salinity salinity_meth Reference or method used in determining salinity salt_regm Information about treatment involving use of salts as supplement to liquid an... samp_capt_status Reason for the sample samp_collec_device The device used to collect an environmental sample samp_collec_method The method employed for collecting the sample samp_collect_point Sampling point on the asset were sample was collected (e samp_dis_stage Stage of the disease at the time of sample collection, e samp_floor The floor of the building, where the sampling room is located samp_loc_corr_rate Metal corrosion rate is the speed of metal deterioration due to environmental... samp_mat_process A brief description of any processing applied to the sample during or after r... samp_md In non deviated well, measured depth is equal to the true vertical depth, TVD... samp_name A local identifier or name that for the material sample used for extracting n... samp_preserv Preservative added to the sample (e samp_room_id Sampling room number samp_size The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... samp_sort_meth Method by which samples are sorted; open face filter collecting total suspend... samp_store_dur Duration for which the sample was stored samp_store_loc Location at which sample was stored, usually name of a specific freezer/room samp_store_temp Temperature at which sample was stored, e samp_subtype Name of sample sub-type samp_taxon_id NCBI taxon id of the sample samp_time_out The recent and long term history of outside sampling samp_transport_cond Sample transport duration (in days or hrs) and temperature the sample was exp... samp_tvdss Depth of the sample i samp_type The type of material from which the sample was obtained samp_vol_we_dna_ext Volume (ml) or mass (g) of total collected sample processed for DNA extractio... samp_weather The weather on the sampling day samp_well_name Name of the well (e sample_collection_day sample_collection_hour sample_collection_minute sample_collection_month sample_collection_site sample_collection_year sample_link A unique identifier to assign parent-child, subsample, or sibling samples sample_shipped The total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent... sample_state_information The chemical phase of a pure sample, or the state of a mixed sample sample_type Type of sample being submitted sampled_portion The portion of the sample that is taken for downstream activity saturates_pc Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that d... scaf_bp Total size in bp of all scaffolds scaf_l50 Given a set of scaffolds, the L50 is defined as the sequence length of the sh... scaf_l90 The L90 statistic is less than or equal to the L50 statistic; it is the lengt... scaf_l_gt50k Total size in bp of all scaffolds greater than 50 KB scaf_logsum The sum of the (length*log(length)) of all scaffolds, times some constant scaf_max Maximum scaffold length scaf_n50 Given a set of scaffolds, each with its own length, the N50 count is defined ... scaf_n90 Given a set of scaffolds, each with its own length, the N90 count is defined ... scaf_n_gt50k Total sequence count of scaffolds greater than 50 KB scaf_pct_gt50k Total sequence size percentage of scaffolds greater than 50 KB scaf_powsum Powersum of all scaffolds is the same as logsum except that it uses the sum o... scaffolds Total sequence count of all scaffolds season The season when sampling occurred season_environment Treatment involving an exposure to a particular season (e season_precpt The average of all seasonal precipitation values known, or an estimated equiv... season_temp Mean seasonal temperature season_use The seasons the space is occupied secondary_treatment The process for substantially degrading the biological content of the sewage sediment_type Information about the sediment type based on major constituents separation_method The method that was used to separate a substance from a solution or mixture seq_meth Sequencing machine used seq_quality_check Indicate if the sequence has been called by automatic systems (none) or under... seqid The ID of the landmark used to establish the coordinate system for the curren... sequencing_field sewage_type Type of wastewater treatment plant as municipial or industrial shad_dev_water_mold Signs of the presence of mold or mildew on the shading device shading_device_cond The physical condition of the shading device at the time of sampling shading_device_loc The location of the shading device in relation to the built structure shading_device_mat The material the shading device is composed of shading_device_type The type of shading device sieving Collection design of pooled samples and/or sieve size and amount of sample si... silicate Concentration of silicate size_frac Filtering pore size used in sample preparation size_frac_low Refers to the mesh/pore size used to pre-filter/pre-sort the sample size_frac_up Refers to the mesh/pore size used to retain the sample slope_aspect The direction a slope faces slope_gradient Commonly called 'slope' sludge_retent_time The time activated sludge remains in reactor smiles A string encoding of a molecular graph, no chiral or isotopic information sodium Sodium concentration in the sample soil_annual_season_temp soil_horizon Specific layer in the land area which measures parallel to the soil surface a... soil_text_measure The relative proportion of different grain sizes of mineral particles in a so... soil_texture_meth Reference or method used in determining soil texture soil_type Description of the soil type or classification soil_type_meth Reference or method used in determining soil series name or other lower-level... solar_irradiance The amount of solar energy that arrives at a specific area of a surface durin... soluble_inorg_mat Concentration of substances such as ammonia, road-salt, sea-salt, cyanide, hy... soluble_iron_micromol soluble_org_mat Concentration of substances such as urea, fruit sugars, soluble proteins, dru... soluble_react_phosp Concentration of soluble reactive phosphorus source_concentration When solutions A (containing substance X) and B are combined together, this s... source_mat_id A unique identifier assigned to a material sample (as defined by http://rs space_typ_state Customary or normal state of the space specific The building specifications specific_ecosystem Specific ecosystems represent specific features of the environment like aphot... specific_humidity The mass of water vapour in a unit mass of moist air, usually expressed as gr... sr_dep_env Source rock depositional environment (https://en sr_geol_age Geological age of source rock (Additional info: https://en sr_kerog_type Origin of kerogen sr_lithology Lithology of source rock (https://en standing_water_regm Treatment involving an exposure to standing water during a plant's life span,... start The start of the feature in positive 1-based integer coordinates start_date The date on which any process or activity was started start_date_inc Date the incubation was started start_time_inc Time the incubation was started started_at_time stationary_phase The material the stationary phase is comprised of used in chromatography storage_process_set This property links a database object to the set of storage processes within ... store_cond Explain how and for how long the soil sample was stored before DNA extraction... strand The strand on which a feature is located stranded_orientation Lists the strand orientiation for a stranded RNA library preparation study_category The type of research initiative study_identifiers study_image Links a study to one or more images study_set This property links a database object to the set of studies within it subject substance_role The role of a substance in a process substances_used The substances that are combined to enable a ChemicalConversionProcess substances_volume The volume of the combined substances that was included in a ChemicalConversi... substructure_type The substructure or under building is that largely hidden section of the buil... subsurface_depth sulfate Concentration of sulfate in the sample sulfate_fw Original sulfate concentration in the hydrocarbon resource sulfide Concentration of sulfide in the sample surf_air_cont Contaminant identified on surface surf_humidity Surfaces: water activity as a function of air and material moisture surf_material Surface materials at the point of sampling surf_moisture Water held on a surface surf_moisture_ph ph measurement of surface surf_temp Temperature of the surface at the time of sampling suspend_part_matter Concentration of suspended particulate matter suspend_solids Concentration of substances including a wide variety of material, such as sil... tan Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by th... target_gene Targeted gene or locus name for marker gene studies target_subfragment Name of subfragment of a gene or locus technical_reps If sending technical replicates of the same sample, indicate the replicate co... temp Temperature of the sample at the time of sampling temp_out The recorded temperature value at sampling time outside temperature The value of a temperature measurement or temperature used in a process term pointer to an ontology class tertiary_treatment The process providing a final treatment stage to raise the effluent quality b... tidal_stage Stage of tide tillage Note method(s) used for tilling tiss_cult_growth_med Description of plant tissue culture growth media used title A name given to the entity that differs from the name/label programmatically ... toluene Concentration of toluene in the sample too_short_contig_num Number of contigs which were excluded from binning for length tot_carb Total carbon content tot_depth_water_col Measurement of total depth of water column tot_diss_nitro Total dissolved nitrogen concentration, reported as nitrogen, measured by: to... tot_inorg_nitro Total inorganic nitrogen content tot_iron Concentration of total iron in the sample tot_nitro Total nitrogen concentration of water samples, calculated by: total nitrogen ... tot_nitro_cont_meth Reference or method used in determining the total nitrogen tot_nitro_content Total nitrogen content of the sample tot_org_c_meth Reference or method used in determining total organic carbon tot_org_carb Definition for soil: total organic carbon content of the soil, definition oth... tot_part_carb Total particulate carbon content tot_phosp Total phosphorus concentration in the sample, calculated by: total phosphorus... tot_phosphate Total amount or concentration of phosphate tot_sulfur Concentration of total sulfur in the sample total_bases Total number of basepairs train_line The subway line name train_stat_loc The train station collection location train_stop_loc The train stop collection location turbidity Measure of the amount of cloudiness or haziness in water caused by individual... tvdss_of_hcr_press True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... tvdss_of_hcr_temp True vertical depth subsea (TVDSS) of the hydrocarbon resource where the orig... typ_occup_density Customary or normal density of occupants type the class_uri of the class that has been instantiated unbinned_contig_num Number of contigs which did not end up in a medium or high quality bin url uses_calibration calibration information is used by a process value vendor ventilation_rate Ventilation rate of the system in the sampled premises ventilation_type Ventilation system used in the sampled premises version vfa Concentration of Volatile Fatty Acids in the sample vfa_fw Original volatile fatty acid concentration in the hydrocarbon resource vis_media The building visual media viscosity A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020t... volatile_org_comp Concentration of carbon-based chemicals that easily evaporate at room tempera... volume The volume of a substance wall_area The total area of the sampled room's walls wall_const_type The building class of the wall defined by the composition of the building ele... wall_finish_mat The material utilized to finish the outer most layer of the wall wall_height The average height of the walls in the sampled room wall_loc The relative location of the wall within the room wall_surf_treatment The surface treatment of interior wall wall_texture The feel, appearance, or consistency of a wall surface wall_thermal_mass The ability of the wall to provide inertia against temperature fluctuations wall_water_mold Signs of the presence of mold or mildew on a wall was_generated_by was_informed_by wastewater_type The origin of wastewater such as human waste, rainfall, storm drains, etc water_cont_soil_meth Reference or method used in determining the water content of soil water_content Water content measurement water_current Measurement of magnitude and direction of flow within a fluid water_cut Current amount of water (%) in a produced fluid stream; or the average of the... water_feat_size The size of the water feature water_feat_type The type of water feature present within the building being sampled water_prod_rate Water production rates per well (e water_temp_regm Information about treatment involving an exposure to water with varying degre... watering_regm Information about treatment involving an exposure to watering frequencies, tr... websites A list of websites that are associated with the entity weekday The day of the week when sampling occurred win A unique identifier of a well or wellbore wind_direction Wind direction is the direction from which a wind originates wind_speed Speed of wind measured at the time of sampling window_cond The physical condition of the window at the time of sampling window_cover The type of window covering window_horiz_pos The horizontal position of the window on the wall window_loc The relative location of the window within the room window_mat The type of material used to finish a window window_open_freq The number of times windows are opened per week window_size The window's length and width window_status Defines whether the windows were open or closed during environmental testing window_type The type of windows window_vert_pos The vertical position of the window on the wall window_water_mold Signs of the presence of mold or mildew on the window workflow_execution_set This property links a database object to the set of workflow executions xylene Concentration of xylene in the sample zinc Concentration of zinc in the sample"},{"location":"#enumerations","title":"Enumerations","text":"Enumeration Description AnalysisTypeEnum ArchStrucEnum BinQualityEnum BiolStatEnum BiosampleCategoryEnum Funding-based, sample location-based, or experimental method-based defined ca... BioticRelationshipEnum BuildDocsEnum BuildOccupTypeEnum BuildingSettingEnum CalibrationStandardEnum CalibrationTargetEnum CeilCondEnum CeilFinishMatEnum CeilTextureEnum CeilTypeEnum ChemicalConversionCategoryEnum ChemicalEntityEnum ChromatographicCategoryEnum ContainerCategoryEnum The permitted types of containers used in processing metabolomic samples CreditEnum CurLandUseEnum DataCategoryEnum DeposEnvEnum DNASampleFormatEnum DoiCategoryEnum DoiProviderEnum DoorCompTypeEnum DoorCondEnum DoorDirectEnum DoorLocEnum DoorMatEnum DoorMoveEnum DoorTypeEnum DoorTypeMetalEnum DoorTypeWoodEnum DrainageClassEnum DrawingsEnum EluentIntroductionCategoryEnum ExecutionResourceEnum ExtWallOrientEnum ExtWindowOrientEnum ExtractionTargetEnum FailureWhatEnum The permitted values for describing where a failure occurred during processin... FailureWhereEnum The permitted values for describing where in the process, either a lab or ana... FaoClassEnum FileTypeEnum FilterTypeEnum FloorCondEnum FloorFinishMatEnum FloorStrucEnum FloorWaterMoldEnum FreqCleanEnum FurnitureEnum GenderRestroomEnum GrowthHabitEnum HandidnessEnum HcProducedEnum HcrEnum HcrGeolAgeEnum HeatCoolTypeEnum HeatDelivLocEnum HostSexEnum IndoorSpaceEnum IndoorSurfEnum InstrumentModelEnum InstrumentVendorEnum IntWallCondEnum IonizationSourceEnum JgiContTypeEnum LibraryTypeEnum LightTypeEnum LithologyEnum ManifestCategoryEnum A list of contexts in which some DataObjects can be analyzed together MassAnalyzerEnum MassSpectrometryAcquisitionStrategyEnum MassSpectrometryEnum MassSpectrumCollectionModeEnum MechStrucEnum MetaproteomicsAnalysisCategoryEnum The category of metaproteomics analysis being performed NucleotideSequencingEnum OccupDocumentEnum OrganismCountEnum OxyStatSampEnum PlantGrowthMedEnum PlantSexEnum PolarityModeEnum ProcessingInstitutionEnum ProfilePositionEnum ProtocolCategoryEnum The possible protocols that may be followed for an assay QuadPosEnum RelSampLocEnum ResolutionCategoryEnum RNASampleFormatEnum RoomCondtEnum RoomConnectedEnum RoomLocEnum RoomSampPosEnum RoomTypeEnum SampCaptStatusEnum SampCollectPointEnum SampDisStageEnum SampFloorEnum SampMdEnum SampSubtypeEnum SampWeatherEnum SamplePortionEnum SampleStateEnum SampleTypeEnum SeasonUseEnum SedimentTypeEnum SeparationMethodEnum The tool/substance used to separate or filter a solution or mixture ShadingDeviceCondEnum ShadingDeviceTypeEnum SoilHorizonEnum SpecificEnum SrDepEnvEnum SrGeolAgeEnum SrKerogTypeEnum SrLithologyEnum StationaryPhaseEnum The type of stationary phase used in a chromatography process StatusEnum StrandedOrientationEnum This enumeration specifies information about stranded RNA library preparation... StudyCategoryEnum SubstanceRoleEnum SubstructureTypeEnum SurfAirContEnum SurfMaterialEnum TargetGeneEnum TidalStageEnum TillageEnum TrainLineEnum TrainStatLocEnum TrainStopLocEnum VisMediaEnum WallConstTypeEnum WallFinishMatEnum WallLocEnum WallSurfTreatmentEnum WallTextureEnum WaterFeatTypeEnum WeekdayEnum WindowCondEnum WindowCoverEnum WindowHorizPosEnum WindowLocEnum WindowMatEnum WindowTypeEnum WindowVertPosEnum YesNoEnum replaces DnaDnaseEnum and DnaseRnaEnum"},{"location":"#types","title":"Types","text":"Type Description Boolean A binary (true or false) value Bytes An integer value that corresponds to a size in bytes Curie a compact URI Date a date (year, month and day) in an idealized calendar DateOrDatetime Either a date or a datetime Datetime The combination of a date and time Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci... DecimalDegree A decimal degree expresses latitude or longitude as decimal fractions Double A real number that conforms to the xsd:double specification ExternalIdentifier A CURIE representing an external identifier Float A real number that conforms to the xsd:float specification Integer An integer Jsonpath A string encoding a JSON Path Jsonpointer A string encoding a JSON Pointer LanguageCode A language code conforming to ISO_639-1 Ncname Prefix part of CURIE Nodeidentifier A URI, CURIE or BNODE that represents a node in a model Objectidentifier A URI or CURIE that represents an object in the model Sparqlpath A string encoding a SPARQL Property Path String A character string Time A time object represents a (local) time of day, independent of any particular... Unit Uri a complete URI Uriorcurie a URI or a CURIE"},{"location":"#subsets","title":"Subsets","text":"Subset Description"},{"location":"AnalysisTypeEnum/","title":"Enum: AnalysisTypeEnum","text":"URI: AnalysisTypeEnum
"},{"location":"AnalysisTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metabolomics None metagenomics None Standard short-read metagenomic sequencing metagenomics_long_read None Long-read metagenomic sequencing metaproteomics None metatranscriptomics None natural organic matter None bulk chemistry None amplicon sequencing assay OBI:0002767"},{"location":"AnalysisTypeEnum/#slots","title":"Slots","text":"Name Description analysis_type Select all the data types associated or available for this biosample"},{"location":"AnalysisTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"AnalysisTypeEnum/#schema-source","title":"Schema Source","text":"name: AnalysisTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metabolomics:\n text: metabolomics\n metagenomics:\n text: metagenomics\n description: Standard short-read metagenomic sequencing\n title: Metagenomics\n metagenomics_long_read:\n text: metagenomics_long_read\n description: Long-read metagenomic sequencing\n title: Metagenomics (long read)\n metaproteomics:\n text: metaproteomics\n metatranscriptomics:\n text: metatranscriptomics\n natural organic matter:\n text: natural organic matter\n bulk chemistry:\n text: bulk chemistry\n amplicon sequencing assay:\n text: amplicon sequencing assay\n meaning: OBI:0002767\n title: Amplicon sequencing assay\n\nURI: ArchStrucEnum
"},{"location":"ArchStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building None shed None home None"},{"location":"ArchStrucEnum/#slots","title":"Slots","text":"Name Description arch_struc An architectural structure is a human-made, free-standing, immobile outdoor c..."},{"location":"ArchStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ArchStrucEnum/#schema-source","title":"Schema Source","text":"name: arch_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n building:\n text: building\n shed:\n text: shed\n home:\n text: home\n\nThe value for any value of a attribute for a sample. This object can hold both the un-normalized atomic value and the structured value
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:AttributeValue
classDiagram\n class AttributeValue\n click AttributeValue href \"../AttributeValue\"\n AttributeValue <|-- QuantityValue\n click QuantityValue href \"../QuantityValue\"\n AttributeValue <|-- ImageValue\n click ImageValue href \"../ImageValue\"\n AttributeValue <|-- PersonValue\n click PersonValue href \"../PersonValue\"\n AttributeValue <|-- TextValue\n click TextValue href \"../TextValue\"\n AttributeValue <|-- TimestampValue\n click TimestampValue href \"../TimestampValue\"\n AttributeValue <|-- ControlledTermValue\n click ControlledTermValue href \"../ControlledTermValue\"\n AttributeValue <|-- GeolocationValue\n click GeolocationValue href \"../GeolocationValue\"\n\n\n\n AttributeValue : has_raw_value\n\n AttributeValue : type\n\n\n\nname: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- has_raw_value\n- type\nclass_uri: nmdc:AttributeValue\n\nname: AttributeValue\ndescription: The value for any value of a attribute for a sample. This object can\n hold both the un-normalized atomic value and the structured value\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: AttributeValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: AttributeValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:AttributeValue\n\nURI: BinQualityEnum
"},{"location":"BinQualityEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description HQ None Metagenome-assembled genome is high quality based on MIMAG standards (https:/... MQ None Metagenome-assembled genome is medium quality based on MIMAG standards (https... LQ None Metagenome-assembled genome is low quality based on MIMAG standards (https://..."},{"location":"BinQualityEnum/#slots","title":"Slots","text":"Name Description bin_quality The quality of the metagenome-assembled genome based on MIMAG standards (http..."},{"location":"BinQualityEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BinQualityEnum/#schema-source","title":"Schema Source","text":"name: BinQualityEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n HQ:\n text: HQ\n description: Metagenome-assembled genome is high quality based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893)\n aliases:\n - high quality\n MQ:\n text: MQ\n description: Metagenome-assembled genome is medium quality based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893)\n aliases:\n - medium quality\n LQ:\n text: LQ\n description: Metagenome-assembled genome is low quality based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893)\n aliases:\n - low quality\n\nURI: BiolStatEnum
"},{"location":"BiolStatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description wild None natural None semi-natural None inbred line None breeder's line None hybrid None clonal selection None mutant None"},{"location":"BiolStatEnum/#slots","title":"Slots","text":"Name Description biol_stat The level of genome modification"},{"location":"BiolStatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BiolStatEnum/#schema-source","title":"Schema Source","text":"name: biol_stat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n wild:\n text: wild\n natural:\n text: natural\n semi-natural:\n text: semi-natural\n inbred line:\n text: inbred line\n breeder's line:\n text: breeder's line\n hybrid:\n text: hybrid\n clonal selection:\n text: clonal selection\n mutant:\n text: mutant\n\nBiological source material which can be characterized by an experiment.
URI: nmdc:Biosample
Note
Mermaid class diagram too large to render.
"},{"location":"Biosample/#inheritance","title":"Inheritance","text":"name: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A sample contains information about the sequenced source material.\n Samples are associated with checklists, which define the fields used to annotate\n the samples. Samples are always associated with a taxon.\nnotes:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: Sample\nslots:\n- associated_studies\n- biosample_categories\n- collected_from\n- embargoed\n- host_disease_stat\n- host_taxid\n- img_identifiers\n- neon_biosample_identifiers\n- samp_name\n- gold_biosample_identifiers\n- insdc_biosample_identifiers\n- emsl_biosample_identifiers\n- igsn_biosample_identifiers\n- abs_air_humidity\n- add_recov_method\n- additional_info\n- address\n- adj_room\n- aero_struc\n- agrochem_addition\n- air_PM_concen\n- air_temp\n- air_temp_regm\n- al_sat\n- al_sat_meth\n- alkalinity\n- alkalinity_method\n- alkyl_diethers\n- alt\n- aminopept_act\n- ammonium\n- ammonium_nitrogen\n- amount_light\n- ances_data\n- annual_precpt\n- annual_temp\n- antibiotic_regm\n- api\n- arch_struc\n- aromatics_pc\n- asphaltenes_pc\n- atmospheric_data\n- avg_dew_point\n- avg_occup\n- avg_temp\n- bac_prod\n- bac_resp\n- bacteria_carb_prod\n- barometric_press\n- basin\n- bathroom_count\n- bedroom_count\n- benzene\n- biochem_oxygen_dem\n- biocide\n- biocide_admin_method\n- biol_stat\n- biomass\n- biotic_regm\n- biotic_relationship\n- bishomohopanol\n- blood_press_diast\n- blood_press_syst\n- bromide\n- build_docs\n- build_occup_type\n- building_setting\n- built_struc_age\n- built_struc_set\n- built_struc_type\n- calcium\n- carb_dioxide\n- carb_monoxide\n- carb_nitro_ratio\n- ceil_area\n- ceil_cond\n- ceil_finish_mat\n- ceil_struc\n- ceil_texture\n- ceil_thermal_mass\n- ceil_type\n- ceil_water_mold\n- chem_administration\n- chem_mutagen\n- chem_oxygen_dem\n- chem_treat_method\n- chem_treatment\n- chloride\n- chlorophyll\n- climate_environment\n- collection_date\n- conduc\n- cool_syst_id\n- core field\n- crop_rotation\n- cult_root_med\n- cur_land_use\n- cur_vegetation\n- cur_vegetation_meth\n- date_last_rain\n- density\n- depos_env\n- depth\n- dew_point\n- diether_lipids\n- diss_carb_dioxide\n- diss_hydrogen\n- diss_inorg_carb\n- diss_inorg_nitro\n- diss_inorg_phosp\n- diss_iron\n- diss_org_carb\n- diss_org_nitro\n- diss_oxygen\n- diss_oxygen_fluid\n- dna_cont_well\n- door_comp_type\n- door_cond\n- door_direct\n- door_loc\n- door_mat\n- door_move\n- door_size\n- door_type\n- door_type_metal\n- door_type_wood\n- door_water_mold\n- down_par\n- drainage_class\n- drawings\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- efficiency_percent\n- elev\n- elevator\n- emulsions\n- env_broad_scale\n- env_local_scale\n- env_medium\n- env_package\n- environment field\n- escalator\n- ethylbenzene\n- exp_duct\n- exp_pipe\n- experimental_factor\n- ext_door\n- ext_wall_orient\n- ext_window_orient\n- extreme_event\n- fao_class\n- fertilizer_regm\n- field\n- filter_type\n- fire\n- fireplace_type\n- flooding\n- floor_age\n- floor_area\n- floor_cond\n- floor_count\n- floor_finish_mat\n- floor_struc\n- floor_thermal_mass\n- floor_water_mold\n- fluor\n- freq_clean\n- freq_cook\n- fungicide_regm\n- furniture\n- gaseous_environment\n- gaseous_substances\n- gender_restroom\n- genetic_mod\n- geo_loc_name\n- glucosidase_act\n- gravidity\n- gravity\n- growth_facil\n- growth_habit\n- growth_hormone_regm\n- hall_count\n- handidness\n- hc_produced\n- hcr\n- hcr_fw_salinity\n- hcr_geol_age\n- hcr_pressure\n- hcr_temp\n- heat_cool_type\n- heat_deliv_loc\n- heat_sys_deliv_meth\n- heat_system_id\n- heavy_metals\n- heavy_metals_meth\n- height_carper_fiber\n- herbicide_regm\n- horizon_meth\n- host_age\n- host_body_habitat\n- host_body_product\n- host_body_site\n- host_body_temp\n- host_color\n- host_common_name\n- host_diet\n- host_dry_mass\n- host_family_relation\n- host_genotype\n- host_growth_cond\n- host_height\n- host_last_meal\n- host_length\n- host_life_stage\n- host_phenotype\n- host_sex\n- host_shape\n- host_subject_id\n- host_subspecf_genlin\n- host_substrate\n- host_symbiont\n- host_taxid\n- host_tot_mass\n- host_wet_mass\n- humidity\n- humidity_regm\n- indoor_space\n- indoor_surf\n- indust_eff_percent\n- inorg_particles\n- inside_lux\n- int_wall_cond\n- investigation field\n- iw_bt_date_well\n- iwf\n- last_clean\n- lat_lon\n- lbc_thirty\n- lbceq\n- light_intensity\n- light_regm\n- light_type\n- link_addit_analys\n- link_class_info\n- link_climate_info\n- lithology\n- local_class\n- local_class_meth\n- magnesium\n- manganese\n- max_occup\n- mean_frict_vel\n- mean_peak_frict_vel\n- mech_struc\n- mechanical_damage\n- methane\n- micro_biomass_meth\n- microbial_biomass\n- mineral_nutr_regm\n- misc_param\n- n_alkanes\n- nitrate\n- nitrate_nitrogen\n- nitrite\n- nitrite_nitrogen\n- nitro\n- non_min_nutr_regm\n- nucleic acid sequence source field\n- number_pets\n- number_plants\n- number_resident\n- occup_density_samp\n- occup_document\n- occup_samp\n- org_carb\n- org_count_qpcr_info\n- org_matter\n- org_nitro\n- org_particles\n- organism_count\n- owc_tvdss\n- oxy_stat_samp\n- oxygen\n- part_org_carb\n- part_org_nitro\n- particle_class\n- permeability\n- perturbation\n- pesticide_regm\n- petroleum_hydrocarb\n- ph\n- ph_meth\n- ph_regm\n- phaeopigments\n- phosphate\n- phosplipid_fatt_acid\n- photon_flux\n- plant_growth_med\n- plant_product\n- plant_sex\n- plant_struc\n- pollutants\n- porosity\n- potassium\n- pour_point\n- pre_treatment\n- pres_animal_insect\n- pressure\n- prev_land_use_meth\n- previous_land_use\n- primary_prod\n- primary_treatment\n- prod_rate\n- prod_start_date\n- profile_position\n- quad_pos\n- radiation_regm\n- rainfall_regm\n- reactor_type\n- redox_potential\n- rel_air_humidity\n- rel_humidity_out\n- rel_samp_loc\n- reservoir\n- resins_pc\n- room_air_exch_rate\n- room_architec_elem\n- room_condt\n- room_connected\n- room_count\n- room_dim\n- room_door_dist\n- room_door_share\n- room_hallway\n- room_loc\n- room_moist_dam_hist\n- room_net_area\n- room_occup\n- room_samp_pos\n- room_type\n- room_vol\n- room_wall_share\n- room_window_count\n- root_cond\n- root_med_carbon\n- root_med_macronutr\n- root_med_micronutr\n- root_med_ph\n- root_med_regl\n- root_med_solid\n- root_med_suppl\n- salinity\n- salinity_meth\n- salt_regm\n- samp_capt_status\n- samp_collec_device\n- samp_collec_method\n- samp_collect_point\n- samp_dis_stage\n- samp_floor\n- samp_loc_corr_rate\n- samp_mat_process\n- samp_md\n- samp_name\n- samp_preserv\n- samp_room_id\n- samp_size\n- samp_sort_meth\n- samp_store_dur\n- samp_store_loc\n- samp_store_temp\n- samp_subtype\n- samp_taxon_id\n- samp_time_out\n- samp_transport_cond\n- samp_tvdss\n- samp_type\n- samp_weather\n- samp_well_name\n- saturates_pc\n- season\n- season_environment\n- season_precpt\n- season_temp\n- season_use\n- secondary_treatment\n- sediment_type\n- sequencing field\n- sewage_type\n- shad_dev_water_mold\n- shading_device_cond\n- shading_device_loc\n- shading_device_mat\n- shading_device_type\n- sieving\n- silicate\n- size_frac\n- size_frac_low\n- size_frac_up\n- slope_aspect\n- slope_gradient\n- sludge_retent_time\n- sodium\n- soil_horizon\n- soil_text_measure\n- soil_texture_meth\n- soil_type\n- soil_type_meth\n- solar_irradiance\n- soluble_inorg_mat\n- soluble_org_mat\n- soluble_react_phosp\n- source_mat_id\n- space_typ_state\n- specific\n- specific_ecosystem\n- specific_humidity\n- sr_dep_env\n- sr_geol_age\n- sr_kerog_type\n- sr_lithology\n- standing_water_regm\n- store_cond\n- substructure_type\n- sulfate\n- sulfate_fw\n- sulfide\n- surf_air_cont\n- surf_humidity\n- surf_material\n- surf_moisture\n- surf_moisture_ph\n- surf_temp\n- suspend_part_matter\n- suspend_solids\n- tan\n- temp\n- temp_out\n- tertiary_treatment\n- tidal_stage\n- tillage\n- tiss_cult_growth_med\n- toluene\n- tot_carb\n- tot_depth_water_col\n- tot_diss_nitro\n- tot_inorg_nitro\n- tot_iron\n- tot_nitro\n- tot_nitro_cont_meth\n- tot_nitro_content\n- tot_org_c_meth\n- tot_org_carb\n- tot_part_carb\n- tot_phosp\n- tot_phosphate\n- tot_sulfur\n- train_line\n- train_stat_loc\n- train_stop_loc\n- turbidity\n- tvdss_of_hcr_press\n- tvdss_of_hcr_temp\n- typ_occup_density\n- ventilation_rate\n- ventilation_type\n- vfa\n- vfa_fw\n- vis_media\n- viscosity\n- volatile_org_comp\n- wall_area\n- wall_const_type\n- wall_finish_mat\n- wall_height\n- wall_loc\n- wall_surf_treatment\n- wall_texture\n- wall_thermal_mass\n- wall_water_mold\n- wastewater_type\n- water_cont_soil_meth\n- water_content\n- water_current\n- water_cut\n- water_feat_size\n- water_feat_type\n- water_prod_rate\n- water_temp_regm\n- watering_regm\n- weekday\n- win\n- wind_direction\n- wind_speed\n- window_cond\n- window_cover\n- window_horiz_pos\n- window_loc\n- window_mat\n- window_open_freq\n- window_size\n- window_status\n- window_type\n- window_vert_pos\n- window_water_mold\n- xylene\n- zinc\n- ecosystem\n- ecosystem_category\n- ecosystem_type\n- ecosystem_subtype\n- specific_ecosystem\n- add_date\n- community\n- habitat\n- host_name\n- location\n- mod_date\n- ncbi_taxonomy_name\n- proport_woa_temperature\n- salinity_category\n- sample_collection_site\n- soluble_iron_micromol\n- subsurface_depth\n- air_temp_regm\n- biotic_regm\n- biotic_relationship\n- climate_environment\n- experimental_factor\n- gaseous_environment\n- growth_facil\n- humidity_regm\n- light_regm\n- phosphate\n- samp_collec_method\n- samp_size\n- source_mat_id\n- watering_regm\n- dna_absorb1\n- dna_absorb2\n- dna_collect_site\n- dna_concentration\n- dna_cont_type\n- dna_cont_well\n- dna_container_id\n- dna_dnase\n- dna_isolate_meth\n- dna_organisms\n- dna_project_contact\n- dna_samp_id\n- dna_sample_format\n- dna_sample_name\n- dna_seq_project\n- dna_seq_project_pi\n- dna_seq_project_name\n- dna_volume\n- proposal_dna\n- dnase_rna\n- proposal_rna\n- rna_absorb1\n- rna_absorb2\n- rna_collect_site\n- rna_concentration\n- rna_cont_type\n- rna_cont_well\n- rna_container_id\n- rna_isolate_meth\n- rna_organisms\n- rna_project_contact\n- rna_samp_id\n- rna_sample_format\n- rna_sample_name\n- rna_seq_project\n- rna_seq_project_pi\n- rna_seq_project_name\n- rna_volume\n- collection_date_inc\n- collection_time\n- collection_time_inc\n- experimental_factor_other\n- filter_method\n- isotope_exposure\n- micro_biomass_c_meth\n- micro_biomass_n_meth\n- microbial_biomass_c\n- microbial_biomass_n\n- non_microb_biomass\n- non_microb_biomass_method\n- org_nitro_method\n- other_treatment\n- start_date_inc\n- start_time_inc\n- project_id\n- replicate_number\n- sample_shipped\n- sample_type\n- technical_reps\n- analysis_type\n- sample_link\n- bulk_elect_conductivity\n- infiltrations\n- zinc\n- manganese\n- ammonium_nitrogen\n- nitrate_nitrogen\n- nitrite_nitrogen\n- lbc_thirty\n- lbceq\nslot_usage:\n collected_from:\n name: collected_from\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n elev:\n name: elev\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n range: float\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n alternative_identifiers:\n name: alternative_identifiers\n description: A uriorcurie reference to an external database or resource that provides\n additional information or context about a specific entity at NMDC.\n multivalued: true\n lat_lon:\n name: lat_lon\n notes:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n env_broad_scale:\n name: env_broad_scale\n required: true\n env_local_scale:\n name: env_local_scale\n required: true\n env_medium:\n name: env_medium\n required: true\n associated_studies:\n name: associated_studies\n range: Study\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n range: string\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n examples:\n - value: 1980-05-18, volcanic eruption\n range: string\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n slope_gradient:\n name: slope_gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n annual_precpt:\n name: annual_precpt\n examples:\n - value: 8.94 inch\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n todos:\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n cur_vegetation_meth:\n name: cur_vegetation_meth\n todos:\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n heavy_metals_meth:\n name: heavy_metals_meth\n title: heavy metals method/ extreme unusual properties\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n multivalued: true\n season_precpt:\n name: season_precpt\n title: average seasonal precipitation\n todos:\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n water_cont_soil_meth:\n name: water_cont_soil_meth\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n range: string\n multivalued: true\n ph_meth:\n name: ph_meth\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n tot_carb:\n name: tot_carb\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n tot_nitro_content:\n name: tot_nitro_content\n examples:\n - value: 5 mg N/ L\n tot_org_c_meth:\n name: tot_org_c_meth\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n tot_org_carb:\n name: tot_org_carb\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n salinity_meth:\n name: salinity_meth\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n sieving:\n name: sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n climate_environment:\n name: climate_environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n gaseous_environment:\n name: gaseous_environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n watering_regm:\n name: watering_regm\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\nclass_uri: nmdc:Biosample\nunique_keys:\n samp_name_unique_key:\n unique_key_name: samp_name_unique_key\n unique_key_slots:\n - samp_name\nrules:\n- preconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: dna_well_requires_plate\n- preconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n description: DNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: dna_plate_requires_well\n- preconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: rna_well_requires_plate\n- preconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n description: RNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: rna_plate_requires_well\n\nname: Biosample\ndescription: Biological source material which can be characterized by an experiment.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A sample contains information about the sequenced source material.\n Samples are associated with checklists, which define the fields used to annotate\n the samples. Samples are always associated with a taxon.\nnotes:\n- could add GOLD and EBI's biosample definitions to the alt_descriptions?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample\n- material sample\n- specimen\n- biospecimen\nexact_mappings:\n- OBI:0000747\n- NCIT:C43412\n- http://purl.obolibrary.org/obo/FBcv_0003024\nis_a: Sample\nslot_usage:\n collected_from:\n name: collected_from\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n elev:\n name: elev\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n range: float\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n alternative_identifiers:\n name: alternative_identifiers\n description: A uriorcurie reference to an external database or resource that provides\n additional information or context about a specific entity at NMDC.\n multivalued: true\n lat_lon:\n name: lat_lon\n notes:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n env_broad_scale:\n name: env_broad_scale\n required: true\n env_local_scale:\n name: env_local_scale\n required: true\n env_medium:\n name: env_medium\n required: true\n associated_studies:\n name: associated_studies\n range: Study\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n range: string\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n range: string\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n examples:\n - value: 1980-05-18, volcanic eruption\n range: string\n slope_aspect:\n name: slope_aspect\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n slope_gradient:\n name: slope_gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n al_sat:\n name: al_sat\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n al_sat_meth:\n name: al_sat_meth\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n annual_precpt:\n name: annual_precpt\n examples:\n - value: 8.94 inch\n cur_vegetation:\n name: cur_vegetation\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n todos:\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n cur_vegetation_meth:\n name: cur_vegetation_meth\n todos:\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n heavy_metals:\n name: heavy_metals\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n heavy_metals_meth:\n name: heavy_metals_meth\n title: heavy metals method/ extreme unusual properties\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n multivalued: true\n season_precpt:\n name: season_precpt\n title: average seasonal precipitation\n todos:\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n water_cont_soil_meth:\n name: water_cont_soil_meth\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n range: string\n multivalued: true\n ph_meth:\n name: ph_meth\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n tot_carb:\n name: tot_carb\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n tot_nitro_content:\n name: tot_nitro_content\n examples:\n - value: 5 mg N/ L\n tot_org_c_meth:\n name: tot_org_c_meth\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n tot_org_carb:\n name: tot_org_carb\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n salinity_meth:\n name: salinity_meth\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n sieving:\n name: sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n climate_environment:\n name: climate_environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n gaseous_environment:\n name: gaseous_environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n watering_regm:\n name: watering_regm\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n source_mat_id:\n name: source_mat_id\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\nattributes:\n associated_studies:\n name: associated_studies\n description: The study associated with a resource.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: associated_studies\n owner: Biosample\n domain_of:\n - Biosample\n - DataGeneration\n range: Study\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n biosample_categories:\n name: biosample_categories\n title: Categories the biosample belongs to\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: biosample_categories\n owner: Biosample\n domain_of:\n - Biosample\n range: BiosampleCategoryEnum\n multivalued: true\n collected_from:\n name: collected_from\n description: The Site from which a Biosample was collected\n todos:\n - add an OBO slot_uri ?\n comments:\n - this illustrates implementing a Biosample relation with a (binary) slot\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: collected_from\n owner: Biosample\n domain_of:\n - Biosample\n range: FieldResearchSite\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n embargoed:\n name: embargoed\n description: If true, the data are embargoed and not available for public access.\n todos:\n - make this required?\n - first apply to Biosample\n - try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n - applying to a Study may not be granular enough\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: embargoed\n owner: Biosample\n domain_of:\n - Biosample\n range: boolean\n recommended: true\n host_disease_stat:\n name: host_disease_stat\n annotations:\n expected_value:\n tag: expected_value\n value: disease name or Disease Ontology term\n description: List of diseases with which the host has been diagnosed; can include\n multiple diagnoses. The value of the field depends on host; for humans the terms\n should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,\n non-human host diseases are free text\n title: host disease status\n examples:\n - value: rabies [DOID:11260]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host disease status\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000031\n alias: host_disease_stat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_taxid:\n name: host_taxid\n annotations:\n expected_value:\n tag: expected_value\n value: NCBI taxon identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: NCBI taxon id of the host, e.g. 9606\n title: host taxid\n comments:\n - Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host taxid\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000250\n alias: host_taxid\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n multivalued: false\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: Biosample\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n neon_biosample_identifiers:\n name: neon_biosample_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - neon_identifiers\n alias: neon_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n samp_name:\n name: samp_name\n annotations:\n expected_value:\n tag: expected_value\n value: text\n description: A local identifier or name that for the material sample used for\n extracting nucleic acids, and subsequent sequencing. It can refer either to\n the original material collected or to any derived sub-samples. It can have any\n format, but we suggest that you make it concise, unique and consistent within\n your lab, and as informative as possible. INSDC requires every sample name from\n a single Submitter to be unique. Use of a globally unique identifier for the\n field source_mat_id is recommended in addition to sample_name.\n title: sample name\n examples:\n - value: ISDsoil1\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample name\n rank: 1000\n is_a: investigation field\n string_serialization: '{text}'\n slot_uri: MIXS:0001107\n alias: samp_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n gold_biosample_identifiers:\n name: gold_biosample_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the GOLD biosample IDs associated with this biosample.\n description: Unique identifier for a biosample submitted to GOLD that matches\n the NMDC submitted biosample\n comments:\n - This is the ID provided by GOLD that starts with 'GB'\n examples:\n - value: https://bioregistry.io/gold:Gb0312930\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - gold_identifiers\n alias: gold_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: uriorcurie\n multivalued: true\n pattern: ^gold:Gb[0-9]+$\n insdc_biosample_identifiers:\n name: insdc_biosample_identifiers\n description: identifiers for corresponding sample in INSDC\n examples:\n - value: https://bioregistry.io/biosample:SAMEA5989477\n - value: https://bioregistry.io/biosample:SAMD00212331\n description: I13_N_5-10 sample from Soil fungal diversity along elevational\n gradients\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/bioregistry/bioregistry/issues/108\n - https://www.ebi.ac.uk/biosamples/\n - https://www.ncbi.nlm.nih.gov/biosample\n - https://www.ddbj.nig.ac.jp/biosample/index-e.html\n aliases:\n - EBI biosample identifiers\n - NCBI biosample identifiers\n - DDBJ biosample identifiers\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n multivalued: true\n pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n emsl_biosample_identifiers:\n name: emsl_biosample_identifiers\n description: A list of identifiers for the biosample from the EMSL database. This\n is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n EMSL NEXUS database.\n title: EMSL Biosample Identifiers\n todos:\n - removed \"planned\" once NEXUS is online\n - determine real expansion for emsl prefix\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - emsl_identifiers\n alias: emsl_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n igsn_biosample_identifiers:\n name: igsn_biosample_identifiers\n description: A list of identifiers for the biosample from the IGSN database.\n title: IGSN Biosample Identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: biosample_identifiers\n mixins:\n - igsn_identifiers\n alias: igsn_biosample_identifiers\n owner: Biosample\n domain_of:\n - Biosample\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n abs_air_humidity:\n name: abs_air_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram, kilogram per kilogram, kilogram, pound\n occurrence:\n tag: occurrence\n value: '1'\n description: Actual mass of water vapor - mh20 - present in the air water vapor\n mixture\n title: absolute air humidity\n examples:\n - value: 9 gram per gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - absolute air humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000122\n alias: abs_air_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n add_recov_method:\n name: add_recov_method\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n for increase of hydrocarbon recovery from resource and start date for each one\n of them. If \"other\" is specified, please propose entry in \"additional info\"\n field\n title: secondary and tertiary recovery methods and start date\n examples:\n - value: Polymer Addition;2018-06-21T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - secondary and tertiary recovery methods and start date\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001009\n alias: add_recov_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n additional_info:\n name: additional_info\n annotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information that doesn't fit anywhere else. Can also be used to propose\n new entries for fields with controlled vocabulary\n title: additional info\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - additional info\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000300\n alias: additional_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n address:\n name: address\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The street name and building number where the sampling occurred.\n title: address\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - address\n rank: 1000\n is_a: core field\n string_serialization: '{integer}{text}'\n slot_uri: MIXS:0000218\n alias: address\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n adj_room:\n name: adj_room\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of rooms (room number, room name) immediately adjacent to the\n sampling room\n title: adjacent rooms\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - adjacent rooms\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000219\n alias: adj_room\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n aero_struc:\n name: aero_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Aerospace structures typically consist of thin plates with stiffeners\n for the external surfaces, bulkheads and frames to support the shape and fasteners\n such as welds, rivets, screws and bolts to hold the components together\n title: aerospace structure\n examples:\n - value: plane\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aerospace structure\n rank: 1000\n is_a: core field\n string_serialization: '[plane|glider]'\n slot_uri: MIXS:0000773\n alias: aero_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n agrochem_addition:\n name: agrochem_addition\n annotations:\n expected_value:\n tag: expected_value\n value: agrochemical name;agrochemical amount;timestamp\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Addition of fertilizers, pesticides, etc. - amount and time of applications\n title: history/agrochemical additions\n examples:\n - value: roundup;5 milligram per liter;2018-06-21\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/agrochemical additions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{timestamp}'\n slot_uri: MIXS:0000639\n alias: agrochem_addition\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n air_PM_concen:\n name: air_PM_concen\n annotations:\n expected_value:\n tag: expected_value\n value: particulate matter name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrograms per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances that remain suspended in the air, and\n comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can\n report multiple PM's by entering numeric values preceded by name of PM\n title: air particulate matter concentration\n examples:\n - value: PM2.5;10 microgram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air particulate matter concentration\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000108\n alias: air_PM_concen\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n air_temp:\n name: air_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature of the air at the time of sampling\n title: air temperature\n examples:\n - value: 20 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000124\n alias: air_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n air_temp_regm:\n name: air_temp_regm\n annotations:\n expected_value:\n tag: expected_value\n value: temperature value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to varying temperatures;\n should include the temperature, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include different temperature regimens\n title: air temperature regimen\n examples:\n - value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - air temperature regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000551\n alias: air_temp_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n al_sat:\n name: al_sat\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative abundance of aluminum in the sample\n title: aluminum saturation/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n notes:\n - Aluminum saturation is the percentage of the CEC occupies by aluminum. Like\n all cations, aluminum held by the cation exchange complex is in equilibrium\n with aluminum in the soil solution.\n examples:\n - value: 27%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - extreme_unusual_properties/Al saturation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000607\n alias: al_sat\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n al_sat_meth:\n name: al_sat_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or URL\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining Aluminum saturation\n title: aluminum saturation method/ extreme unusual properties\n todos:\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n comments:\n - Required when aluminum saturation is provided.\n examples:\n - value: https://doi.org/10.1371/journal.pone.0176357\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - extreme_unusual_properties/Al saturation method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000324\n alias: al_sat_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n alkalinity:\n name: alkalinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliequivalent per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Alkalinity, the ability of a solution to neutralize acids to the\n equivalence point of carbonate or bicarbonate\n title: alkalinity\n examples:\n - value: 50 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkalinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000421\n alias: alkalinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n alkalinity_method:\n name: alkalinity_method\n annotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: '1'\n description: Method used for alkalinity measurement\n title: alkalinity method\n examples:\n - value: titration\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkalinity method\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000298\n alias: alkalinity_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n alkyl_diethers:\n name: alkyl_diethers\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of alkyl diethers\n title: alkyl diethers\n examples:\n - value: 0.005 mole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - alkyl diethers\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000490\n alias: alkyl_diethers\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n alt:\n name: alt\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Altitude is a term used to identify heights of objects such as airplanes,\n space shuttles, rockets, atmospheric balloons and heights of places such as\n atmospheric layers and clouds. It is used to measure the height of an object\n which is above the earth's surface. In this context, the altitude measurement\n is the vertical distance between the earth's surface above sea level and the\n sampled position in the air\n title: altitude\n examples:\n - value: 100 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - altitude\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000094\n alias: alt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n aminopept_act:\n name: aminopept_act\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of aminopeptidase activity\n title: aminopeptidase activity\n examples:\n - value: 0.269 mole per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aminopeptidase activity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000172\n alias: aminopept_act\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ammonium:\n name: ammonium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ammonium in the sample\n title: ammonium\n examples:\n - value: 1.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ammonium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000427\n alias: ammonium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ammonium_nitrogen:\n name: ammonium_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ammonium nitrogen in the sample\n title: ammonium nitrogen\n examples:\n - value: 2.3 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - ammonium_nitrogen\n - NH4-N\n rank: 1000\n alias: ammonium_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n amount_light:\n name: amount_light\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux, lumens per square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The unit of illuminance and luminous emittance, measuring luminous\n flux per unit area\n title: amount of light\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - amount of light\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000140\n alias: amount_light\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ances_data:\n name: ances_data\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about either pedigree or other ancestral information\n description (e.g. parental variety in case of mutant or selection), e.g. A/3*B\n (meaning [(A x B) x B] x B)\n title: ancestral data\n examples:\n - value: A/3*B\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ancestral data\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000247\n alias: ances_data\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n annual_precpt:\n name: annual_precpt\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of all annual precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\n title: mean annual precipitation\n examples:\n - value: 8.94 inch\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean annual precipitation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000644\n alias: annual_precpt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n annual_temp:\n name: annual_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Mean annual temperature\n title: mean annual temperature\n examples:\n - value: 12.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean annual temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000642\n alias: annual_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n antibiotic_regm:\n name: antibiotic_regm\n annotations:\n expected_value:\n tag: expected_value\n value: antibiotic name;antibiotic amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving antibiotic administration;\n should include the name of antibiotic, amount administered, treatment regimen\n including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n antibiotic regimens\n title: antibiotic regimen\n examples:\n - value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - antibiotic regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000553\n alias: antibiotic_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n api:\n name: api\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degrees API\n occurrence:\n tag: occurrence\n value: '1'\n description: 'API gravity is a measure of how heavy or light a petroleum liquid\n is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g.\n 31.1\u00ac\u221e API)'\n title: API gravity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - API gravity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000157\n alias: api\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n arch_struc:\n name: arch_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: An architectural structure is a human-made, free-standing, immobile\n outdoor construction\n title: architectural structure\n examples:\n - value: shed\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - architectural structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000774\n alias: arch_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: arch_struc_enum\n multivalued: false\n aromatics_pc:\n name: aromatics_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: aromatics wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - aromatics wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000133\n alias: aromatics_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n asphaltenes_pc:\n name: asphaltenes_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: asphaltenes wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - asphaltenes wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000135\n alias: asphaltenes_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n atmospheric_data:\n name: atmospheric_data\n annotations:\n expected_value:\n tag: expected_value\n value: atmospheric data name;measurement value\n occurrence:\n tag: occurrence\n value: m\n description: Measurement of atmospheric data; can include multiple data\n title: atmospheric data\n examples:\n - value: wind speed;9 knots\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - atmospheric data\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0001097\n alias: atmospheric_data\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n avg_dew_point:\n name: avg_dew_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of dew point measures taken at the beginning of every\n hour over a 24 hour period on the sampling day\n title: average dew point\n examples:\n - value: 25.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average dew point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000141\n alias: avg_dew_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n avg_occup:\n name: avg_occup\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Daily average occupancy of room. Indicate the number of person(s)\n daily occupying the sampling room.\n title: average daily occupancy\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average daily occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000775\n alias: avg_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n avg_temp:\n name: avg_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of temperatures taken at the beginning of every hour\n over a 24 hour period on the sampling day\n title: average temperature\n examples:\n - value: 12.5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - average temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000142\n alias: avg_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n bac_prod:\n name: bac_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Bacterial production in the water column measured by isotope uptake\n title: bacterial production\n examples:\n - value: 5 milligram per cubic meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000683\n alias: bac_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n bac_resp:\n name: bac_resp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, micromole oxygen per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of bacterial respiration in the water column\n title: bacterial respiration\n examples:\n - value: 300 micromole oxygen per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial respiration\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000684\n alias: bac_resp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n bacteria_carb_prod:\n name: bacteria_carb_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of bacterial carbon production\n title: bacterial carbon production\n examples:\n - value: 2.53 microgram per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bacterial carbon production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000173\n alias: bacteria_carb_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n barometric_press:\n name: barometric_press\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millibar\n occurrence:\n tag: occurrence\n value: '1'\n description: Force per unit area exerted against a surface by the weight of air\n above that surface\n title: barometric pressure\n examples:\n - value: 5 millibar\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - barometric pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000096\n alias: barometric_press\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n basin:\n name: basin\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the basin (e.g. Campos)\n title: basin name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - basin name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000290\n alias: basin\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n bathroom_count:\n name: bathroom_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of bathrooms in the building\n title: bathroom count\n examples:\n - value: '1'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bathroom count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000776\n alias: bathroom_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n bedroom_count:\n name: bedroom_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of bedrooms in the building\n title: bedroom count\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bedroom count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000777\n alias: bedroom_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n benzene:\n name: benzene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of benzene in the sample\n title: benzene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - benzene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000153\n alias: benzene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n biochem_oxygen_dem:\n name: biochem_oxygen_dem\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Amount of dissolved oxygen needed by aerobic biological organisms\n in a body of water to break down organic material present in a given water sample\n at certain temperature over a specific time period\n title: biochemical oxygen demand\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biochemical oxygen demand\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000653\n alias: biochem_oxygen_dem\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n biocide:\n name: biocide\n annotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: List of biocides (commercial name of product and supplier) and date\n of administration\n title: biocide administration\n examples:\n - value: ALPHA 1427;Baker Hughes;2008-01-23\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biocide administration\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text};{timestamp}'\n slot_uri: MIXS:0001011\n alias: biocide\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n biocide_admin_method:\n name: biocide_admin_method\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Method of biocide administration (dose, frequency, duration, time\n elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3\n days)\n title: biocide administration method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biocide administration method\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\n slot_uri: MIXS:0000456\n alias: biocide_admin_method\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n biol_stat:\n name: biol_stat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The level of genome modification.\n title: biological status\n examples:\n - value: natural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biological status\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000858\n alias: biol_stat\n owner: Biosample\n domain_of:\n - Biosample\n range: biol_stat_enum\n multivalued: false\n biomass:\n name: biomass\n annotations:\n expected_value:\n tag: expected_value\n value: biomass type;measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram\n occurrence:\n tag: occurrence\n value: m\n description: Amount of biomass; should include the name for the part of biomass\n measured, e.g. Microbial, total. Can include multiple measurements\n title: biomass\n examples:\n - value: total;20 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biomass\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000174\n alias: biomass\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n biotic_regm:\n name: biotic_regm\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about treatment(s) involving use of biotic factors, such\n as bacteria, viruses or fungi.\n title: biotic regimen\n examples:\n - value: sample inoculated with Rhizobium spp. Culture\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - biotic regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001038\n alias: biotic_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n biotic_relationship:\n name: biotic_relationship\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n description: Description of relationship(s) between the subject organism and other\n organism(s) it is associated with. E.g., parasite on species X; mutualist with\n species Y. The target organism is the subject of the relationship, and the other\n organism(s) is the object\n title: observed biotic relationship\n examples:\n - value: free living\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - observed biotic relationship\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000028\n alias: biotic_relationship\n owner: Biosample\n domain_of:\n - Biosample\n range: biotic_relationship_enum\n multivalued: false\n bishomohopanol:\n name: bishomohopanol\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, microgram per gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of bishomohopanol\n title: bishomohopanol\n examples:\n - value: 14 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bishomohopanol\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000175\n alias: bishomohopanol\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n blood_press_diast:\n name: blood_press_diast\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\n description: Resting diastolic blood pressure, measured as mm mercury\n title: host blood pressure diastolic\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host blood pressure diastolic\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000258\n alias: blood_press_diast\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n blood_press_syst:\n name: blood_press_syst\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\n description: Resting systolic blood pressure, measured as mm mercury\n title: host blood pressure systolic\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host blood pressure systolic\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000259\n alias: blood_press_syst\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n bromide:\n name: bromide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of bromide\n title: bromide\n examples:\n - value: 0.05 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - bromide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000176\n alias: bromide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n build_docs:\n name: build_docs\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building design, construction and operation documents\n title: design, construction, and operation documents\n examples:\n - value: maintenance plans\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - design, construction, and operation documents\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000787\n alias: build_docs\n owner: Biosample\n domain_of:\n - Biosample\n range: build_docs_enum\n multivalued: false\n build_occup_type:\n name: build_occup_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: The primary function for which a building or discrete part of a building\n is intended to be used\n title: building occupancy type\n examples:\n - value: market\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - building occupancy type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000761\n alias: build_occup_type\n owner: Biosample\n domain_of:\n - Biosample\n range: build_occup_type_enum\n multivalued: true\n building_setting:\n name: building_setting\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A location (geography) where a building is set\n title: building setting\n examples:\n - value: rural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - building setting\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000768\n alias: building_setting\n owner: Biosample\n domain_of:\n - Biosample\n range: building_setting_enum\n multivalued: false\n built_struc_age:\n name: built_struc_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year\n occurrence:\n tag: occurrence\n value: '1'\n description: The age of the built structure since construction\n title: built structure age\n examples:\n - value: '15'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000145\n alias: built_struc_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n built_struc_set:\n name: built_struc_set\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The characterization of the location of the built structure as high\n or low human density\n title: built structure setting\n examples:\n - value: rural\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure setting\n rank: 1000\n is_a: core field\n string_serialization: '[urban|rural]'\n slot_uri: MIXS:0000778\n alias: built_struc_set\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n built_struc_type:\n name: built_struc_type\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: A physical structure that is a body or assemblage of bodies in space\n to form a system capable of supporting loads\n title: built structure type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - built structure type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000721\n alias: built_struc_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n calcium:\n name: calcium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of calcium in the sample\n title: calcium\n examples:\n - value: 0.2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - calcium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000432\n alias: calcium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n carb_dioxide:\n name: carb_dioxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Carbon dioxide (gas) amount or concentration at the time of sampling\n title: carbon dioxide\n examples:\n - value: 410 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon dioxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000097\n alias: carb_dioxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n carb_monoxide:\n name: carb_monoxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Carbon monoxide (gas) amount or concentration at the time of sampling\n title: carbon monoxide\n examples:\n - value: 0.1 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon monoxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000098\n alias: carb_monoxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n carb_nitro_ratio:\n name: carb_nitro_ratio\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Ratio of amount or concentrations of carbon to nitrogen\n title: carbon/nitrogen ratio\n examples:\n - value: '0.417361111'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - carbon/nitrogen ratio\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000310\n alias: carb_nitro_ratio\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ceil_area:\n name: ceil_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The area of the ceiling space within the room\n title: ceiling area\n examples:\n - value: 25 square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000148\n alias: ceil_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ceil_cond:\n name: ceil_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the ceiling at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: ceiling condition\n examples:\n - value: damaged\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000779\n alias: ceil_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_cond_enum\n multivalued: false\n ceil_finish_mat:\n name: ceil_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material used to finish a ceiling\n title: ceiling finish material\n examples:\n - value: stucco\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000780\n alias: ceil_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_finish_mat_enum\n multivalued: false\n ceil_struc:\n name: ceil_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The construction format of the ceiling\n title: ceiling structure\n examples:\n - value: concrete\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling structure\n rank: 1000\n is_a: core field\n string_serialization: '[wood frame|concrete]'\n slot_uri: MIXS:0000782\n alias: ceil_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n ceil_texture:\n name: ceil_texture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The feel, appearance, or consistency of a ceiling surface\n title: ceiling texture\n examples:\n - value: popcorn\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling texture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000783\n alias: ceil_texture\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_texture_enum\n multivalued: false\n ceil_thermal_mass:\n name: ceil_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the ceiling to provide inertia against temperature\n fluctuations. Generally this means concrete that is exposed. A metal deck that\n supports a concrete slab will act thermally as long as it is exposed to room\n air flow\n title: ceiling thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000143\n alias: ceil_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ceil_type:\n name: ceil_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of ceiling according to the ceiling's appearance or construction\n title: ceiling type\n examples:\n - value: coffered\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000784\n alias: ceil_type\n owner: Biosample\n domain_of:\n - Biosample\n range: ceil_type_enum\n multivalued: false\n ceil_water_mold:\n name: ceil_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the ceiling\n title: ceiling signs of water/mold\n examples:\n - value: presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ceiling signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000781\n alias: ceil_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n chem_administration:\n name: chem_administration\n annotations:\n expected_value:\n tag: expected_value\n value: CHEBI;timestamp\n occurrence:\n tag: occurrence\n value: m\n description: List of chemical compounds administered to the host or site where\n sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can\n include multiple compounds. For chemical entities of biological interest ontology\n (chebi) (v 163), http://purl.bioontology.org/ontology/chebi\n title: chemical administration\n examples:\n - value: agar [CHEBI:2509];2018-05-11T20:00Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical administration\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]};{timestamp}'\n slot_uri: MIXS:0000751\n alias: chem_administration\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n chem_mutagen:\n name: chem_mutagen\n annotations:\n expected_value:\n tag: expected_value\n value: mutagen name;mutagen amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving use of mutagens; should include the name of mutagen,\n amount administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple mutagen regimens\n title: chemical mutagen\n examples:\n - value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical mutagen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000555\n alias: chem_mutagen\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n chem_oxygen_dem:\n name: chem_oxygen_dem\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: A measure of the capacity of water to consume oxygen during the decomposition\n of organic matter and the oxidation of inorganic chemicals such as ammonia and\n nitrite\n title: chemical oxygen demand\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical oxygen demand\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000656\n alias: chem_oxygen_dem\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n chem_treat_method:\n name: chem_treat_method\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Method of chemical administration(dose, frequency, duration, time\n elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1\n hr; 0 days)\n title: chemical treatment method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical treatment method\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\n slot_uri: MIXS:0000457\n alias: chem_treat_method\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n chem_treatment:\n name: chem_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: List of chemical compounds administered upstream the sampling location\n where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n demulsifiers, and other production chemicals etc.). The commercial name of the\n product and name of the supplier should be provided. The date of administration\n should also be included\n title: chemical treatment\n examples:\n - value: ACCENT 1125;DOW;2010-11-17\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chemical treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text};{timestamp}'\n slot_uri: MIXS:0001012\n alias: chem_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n chloride:\n name: chloride\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of chloride in the sample\n title: chloride\n examples:\n - value: 5000 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chloride\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000429\n alias: chloride\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n chlorophyll:\n name: chlorophyll\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter, microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of chlorophyll\n title: chlorophyll\n examples:\n - value: 5 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - chlorophyll\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000177\n alias: chlorophyll\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n climate_environment:\n name: climate_environment\n annotations:\n expected_value:\n tag: expected_value\n value: climate name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to a particular climate; treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n climates\n title: climate environment\n todos:\n - description says \"can include multiple climates\" but multivalued is set to false\n - add examples, i need to see some examples to add correctly formatted example.\n examples:\n - value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - climate environment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001040\n alias: climate_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n collection_date:\n name: collection_date\n annotations:\n expected_value:\n tag: expected_value\n value: date and time\n description: 'The time of sampling, either as an instance (single point in time)\n or interval. In case no exact time is available, the date/time can be right\n truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\n title: collection date\n examples:\n - value: 2018-05-11T10:00:00+01:00; 2018-05-11\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - collection date\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000011\n alias: collection_date\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n conduc:\n name: conduc\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliSiemens per centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: Electrical conductivity of water\n title: conductivity\n examples:\n - value: 10 milliSiemens per centimeter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - conductivity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000692\n alias: conduc\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n cool_syst_id:\n name: cool_syst_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: The cooling system identifier\n title: cooling system identifier\n examples:\n - value: '12345'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - cooling system identifier\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000785\n alias: cool_syst_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n core field:\n name: core field\n description: basic fields\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: core_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n crop_rotation:\n name: crop_rotation\n annotations:\n expected_value:\n tag: expected_value\n value: crop rotation status;schedule\n occurrence:\n tag: occurrence\n value: '1'\n description: Whether or not crop is rotated, and if yes, rotation schedule\n title: history/crop rotation\n examples:\n - value: yes;R2/2017-01-01/2018-12-31/P6M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/crop rotation\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000318\n alias: crop_rotation\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n cult_root_med:\n name: cult_root_med\n annotations:\n expected_value:\n tag: expected_value\n value: name, PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Name or reference for the hydroponic or in vitro culture rooting\n medium; can be the name of a commonly used medium or reference to a specific\n medium, e.g. Murashige and Skoog medium. If the medium has not been formally\n published, use the rooting medium descriptors.\n title: culture rooting medium\n examples:\n - value: http://himedialabs.com/TD/PT158.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - culture rooting medium\n rank: 1000\n is_a: core field\n string_serialization: '{text}|{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0001041\n alias: cult_root_med\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n cur_land_use:\n name: cur_land_use\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Present state of sample site\n title: current land use\n examples:\n - value: conifers\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current land use\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001080\n alias: cur_land_use\n owner: Biosample\n domain_of:\n - Biosample\n range: cur_land_use_enum\n multivalued: false\n cur_vegetation:\n name: cur_vegetation\n annotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n title: current vegetation\n todos:\n - Recommend changing this from text value to some king of ontology?\n comments:\n - Values provided here can be specific species of vegetation or vegetation regions\n - See for vegetation regions- https://education.nationalgeographic.org/resource/vegetation-region\n examples:\n - value: deciduous forest\n - value: forest\n - value: Bauhinia variegata\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current vegetation\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000312\n alias: cur_vegetation\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n cur_vegetation_meth:\n name: cur_vegetation_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in vegetation classification\n title: current vegetation method\n todos:\n - I'm not sure this is a DOI, PMID, or URI. Should pool the community and find\n out how they accomplish this if provided.\n comments:\n - Required when current vegetation is provided.\n examples:\n - value: https://doi.org/10.1111/j.1654-109X.2011.01154.x\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current vegetation method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000314\n alias: cur_vegetation_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n date_last_rain:\n name: date_last_rain\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: The date of the last time it rained\n title: date last rain\n examples:\n - value: 2018-05-11:T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - date last rain\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000786\n alias: date_last_rain\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n density:\n name: density\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter, gram per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: Density of the sample, which is its mass per unit volume (aka volumetric\n mass density)\n title: density\n examples:\n - value: 1000 kilogram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - density\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000435\n alias: density\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n depos_env:\n name: depos_env\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: depositional environment\n examples:\n - value: Continental - Alluvial\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depositional environment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000992\n alias: depos_env\n owner: Biosample\n domain_of:\n - Biosample\n range: depos_env_enum\n multivalued: false\n depth:\n name: depth\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: The vertical distance below local surface, e.g. for sediment or soil\n samples depth is measured from sediment or soil surface, respectively. Depth\n can be reported as an interval for subsurface samples.\n title: depth\n examples:\n - value: 10 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000018\n alias: depth\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n dew_point:\n name: dew_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The temperature to which a given parcel of humid air must be cooled,\n at constant barometric pressure, for water vapor to condense into water.\n title: dew point\n examples:\n - value: 22 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dew point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000129\n alias: dew_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diether_lipids:\n name: diether_lipids\n annotations:\n expected_value:\n tag: expected_value\n value: diether lipid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of diether lipids; can include multiple types of diether\n lipids\n title: diether lipids\n examples:\n - value: 0.2 nanogram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - diether lipids\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000178\n alias: diether_lipids\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n diss_carb_dioxide:\n name: diss_carb_dioxide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved carbon dioxide in the sample or liquid\n portion of the sample\n title: dissolved carbon dioxide\n examples:\n - value: 5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved carbon dioxide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000436\n alias: diss_carb_dioxide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_hydrogen:\n name: diss_hydrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved hydrogen\n title: dissolved hydrogen\n examples:\n - value: 0.3 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved hydrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000179\n alias: diss_hydrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_inorg_carb:\n name: diss_inorg_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Dissolved inorganic carbon concentration in the sample, typically\n measured after filtering the sample using a 0.45 micrometer filter\n title: dissolved inorganic carbon\n examples:\n - value: 2059 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000434\n alias: diss_inorg_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_inorg_nitro:\n name: diss_inorg_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved inorganic nitrogen\n title: dissolved inorganic nitrogen\n examples:\n - value: 761 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000698\n alias: diss_inorg_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_inorg_phosp:\n name: diss_inorg_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved inorganic phosphorus in the sample\n title: dissolved inorganic phosphorus\n examples:\n - value: 56.5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved inorganic phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000106\n alias: diss_inorg_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_iron:\n name: diss_iron\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved iron in the sample\n title: dissolved iron\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved iron\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000139\n alias: diss_iron\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_org_carb:\n name: diss_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved organic carbon in the sample, liquid portion\n of the sample, or aqueous phase of the fluid\n title: dissolved organic carbon\n examples:\n - value: 197 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000433\n alias: diss_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_org_nitro:\n name: diss_org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Dissolved organic nitrogen concentration measured as; total dissolved\n nitrogen - NH4 - NO3 - NO2\n title: dissolved organic nitrogen\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000162\n alias: diss_org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_oxygen:\n name: diss_oxygen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved oxygen\n title: dissolved oxygen\n examples:\n - value: 175 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved oxygen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000119\n alias: diss_oxygen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n diss_oxygen_fluid:\n name: diss_oxygen_fluid\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of dissolved oxygen in the oil field produced fluids\n as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\n title: dissolved oxygen in fluids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - dissolved oxygen in fluids\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000438\n alias: diss_oxygen_fluid\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n dna_cont_well:\n name: dna_cont_well\n title: DNA plate position\n comments:\n - Required when 'plate' is selected for container type.\n - Leave blank if the sample will be shipped in a tube.\n - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n pass validation.\n - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n examples:\n - value: B2\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{96 well plate pos}'\n alias: dna_cont_well\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n door_comp_type:\n name: door_comp_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The composite type of the door\n title: door type, composite\n examples:\n - value: revolving\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, composite\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000795\n alias: door_comp_type\n owner: Biosample\n domain_of:\n - Biosample\n range: door_comp_type_enum\n multivalued: false\n door_cond:\n name: door_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The phsical condition of the door\n title: door condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000788\n alias: door_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: door_cond_enum\n multivalued: false\n door_direct:\n name: door_direct\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The direction the door opens\n title: door direction of opening\n examples:\n - value: inward\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door direction of opening\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000789\n alias: door_direct\n owner: Biosample\n domain_of:\n - Biosample\n range: door_direct_enum\n multivalued: false\n door_loc:\n name: door_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the door in the room\n title: door location\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000790\n alias: door_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: door_loc_enum\n multivalued: false\n door_mat:\n name: door_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The material the door is composed of\n title: door material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000791\n alias: door_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: door_mat_enum\n multivalued: false\n door_move:\n name: door_move\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of movement of the door\n title: door movement\n examples:\n - value: swinging\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door movement\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000792\n alias: door_move\n owner: Biosample\n domain_of:\n - Biosample\n range: door_move_enum\n multivalued: false\n door_size:\n name: door_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The size of the door\n title: door area or size\n examples:\n - value: 2.5 square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door area or size\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000158\n alias: door_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n door_type:\n name: door_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of door material\n title: door type\n examples:\n - value: wooden\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000794\n alias: door_type\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_enum\n multivalued: false\n door_type_metal:\n name: door_type_metal\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of metal door\n title: door type, metal\n examples:\n - value: hollow\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, metal\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000796\n alias: door_type_metal\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_metal_enum\n multivalued: false\n door_type_wood:\n name: door_type_wood\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of wood door\n title: door type, wood\n examples:\n - value: battened\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door type, wood\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000797\n alias: door_type_wood\n owner: Biosample\n domain_of:\n - Biosample\n range: door_type_wood_enum\n multivalued: false\n door_water_mold:\n name: door_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on a door\n title: door signs of water/mold\n examples:\n - value: presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - door signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000793\n alias: door_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n down_par:\n name: down_par\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microEinstein per square meter per second, microEinstein per square\n centimeter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Visible waveband radiance and irradiance measurements in the water\n column\n title: downward PAR\n examples:\n - value: 28.71 microEinstein per square meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - downward PAR\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000703\n alias: down_par\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n drainage_class:\n name: drainage_class\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Drainage classification from a standard system such as the USDA system\n title: drainage classification\n examples:\n - value: well\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - drainage classification\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001085\n alias: drainage_class\n owner: Biosample\n domain_of:\n - Biosample\n range: drainage_class_enum\n multivalued: false\n drawings:\n name: drawings\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The buildings architectural drawings; if design is chosen, indicate\n phase-conceptual, schematic, design development, and construction documents\n title: drawings\n examples:\n - value: sketch\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - drawings\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000798\n alias: drawings\n owner: Biosample\n domain_of:\n - Biosample\n range: drawings_enum\n multivalued: false\n ecosystem:\n name: ecosystem\n description: An ecosystem is a combination of a physical environment (abiotic\n factors) and all the organisms (biotic factors) that interact with this environment.\n Ecosystem is in position 1/5 in a GOLD path.\n comments:\n - The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism\n or environmental sample is collected. The three broad groups under Ecosystem\n are Environmental, Host-associated, and Engineered. They represent samples collected\n from a natural environment or from another organism or from engineered environments\n like bioreactors respectively.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_category:\n name: ecosystem_category\n description: Ecosystem categories represent divisions within the ecosystem based\n on specific characteristics of the environment from where an organism or sample\n is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n comments:\n - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or\n phyla and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_category\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_subtype:\n name: ecosystem_subtype\n description: Ecosystem subtypes represent further subdivision of Ecosystem types\n into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n path.\n comments:\n - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n the Ecosystem subtype category.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_subtype\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_type:\n name: ecosystem_type\n description: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still\n broad but specific to the characteristics of a given environment. Ecosystem\n type is in position 3/5 in a GOLD path.\n comments:\n - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_type\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n efficiency_percent:\n name: efficiency_percent\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Percentage of volatile solids removed from the anaerobic digestor\n title: efficiency percent\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - efficiency percent\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000657\n alias: efficiency_percent\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n elev:\n name: elev\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the\n surface, such as an aircraft in flight or a spacecraft in orbit.\n title: elevation, meters\n comments:\n - All elevations must be reported in meters. Provide the numerical portion only.\n - Please use https://www.advancedconverter.com/map-tools/find-altitude-by-coordinates,\n if needed, to help estimate the elevation based on latitude and longitude coordinates.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevation\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000093\n alias: elev\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n multivalued: false\n elevator:\n name: elevator\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of elevators within the built structure\n title: elevator count\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevator count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000799\n alias: elevator\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n emulsions:\n name: emulsions\n annotations:\n expected_value:\n tag: expected_value\n value: emulsion name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Amount or concentration of substances such as paints, adhesives,\n mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion\n types\n title: emulsions\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - emulsions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000660\n alias: emulsions\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n env_broad_scale:\n name: env_broad_scale\n annotations:\n expected_value:\n tag: expected_value\n value: The major environment type(s) where the sample was collected. Recommend\n subclasses of biome [ENVO:00000428]. Multiple terms can be separated by\n one or more pipes.\n tooltip:\n tag: tooltip\n value: The biome or major environmental system where the sample or specimen\n originated. Choose values from subclasses of the 'biome' class [ENVO:00000428]\n in the Environment Ontology (ENVO). For host-associated or plant-associated\n samples, use terms from the UBERON or Plant Ontology to describe the broad\n anatomical or morphological context\n description: 'Report the major environmental system the sample or specimen came\n from. The system(s) identified should have a coarse spatial grain, to provide\n the general environmental context of where the sampling was done (e.g. in the\n desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\n EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\n title: broad-scale environmental context\n examples:\n - value: oceanic epipelagic zone biome [ENVO:01000035]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - broad-scale environmental context\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000012\n alias: env_broad_scale\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n multivalued: false\n env_local_scale:\n name: env_local_scale\n annotations:\n expected_value:\n tag: expected_value\n value: Environmental entities having causal influences upon the entity at\n time of sampling.\n tooltip:\n tag: tooltip\n value: The specific environmental entities or features near the sample or\n specimen that significantly influence its characteristics or composition.\n These entities are typically smaller in scale than the broad environmental\n context. Values for this field should be countable, material nouns and must\n be chosen from subclasses of BFO:0000040 (material entity) that appear in\n the Environment Ontology (ENVO). For host-associated or plant-associated\n samples, use terms from the UBERON or Plant Ontology to describe specific\n anatomical structures or plant parts.\n description: 'Report the entity or entities which are in the sample or specimen\u2019s\n local vicinity and which you believe have significant causal influences on your\n sample or specimen. We recommend using EnvO terms which are of smaller spatial\n grain than your entry for env_broad_scale. Terms, such as anatomical sites,\n from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)\n are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\n title: local environmental context\n examples:\n - value: litter layer [ENVO:01000338]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - local environmental context\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000013\n alias: env_local_scale\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n multivalued: false\n env_medium:\n name: env_medium\n annotations:\n expected_value:\n tag: expected_value\n value: The material displaced by the entity at time of sampling. Recommend\n subclasses of environmental material [ENVO:00010483].\n tooltip:\n tag: tooltip\n value: The predominant environmental material or substrate that directly surrounds\n or hosts the sample or specimen at the time of sampling. Choose values from\n subclasses of the 'environmental material' class [ENVO:00010483] in the\n Environment Ontology (ENVO). Values for this field should be measurable\n or mass material nouns, representing continuous environmental materials.\n For host-associated or plant-associated samples, use terms from the UBERON\n or Plant Ontology to indicate a tissue, organ, or plant structure\n description: 'Report the environmental material(s) immediately surrounding the\n sample or specimen at the time of sampling. We recommend using subclasses of\n ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO\n documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n . Terms from other OBO ontologies are permissible as long as they reference\n mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities\n (e.g. a tree, a leaf, a table top).'\n title: environmental medium\n examples:\n - value: soil [ENVO:00001998]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - environmental medium\n rank: 1000\n is_a: environment field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000014\n alias: env_medium\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n required: true\n multivalued: false\n env_package:\n name: env_package\n description: MIxS extension for reporting of measurements and observations obtained\n from one or more of the environments where the sample was obtained. All environmental\n packages listed here are further defined in separate subtables. By giving the\n name of the environmental package, a selection of fields can be made from the\n subtables and can be reported\n notes:\n - no longer in MIxS as of 6.0?\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - environmental package\n rank: 1000\n alias: env_package\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n environment field:\n name: environment field\n description: field describing environmental aspect of a sample\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: environment_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n escalator:\n name: escalator\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of escalators within the built structure\n title: escalator count\n examples:\n - value: '4'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - escalator count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000800\n alias: escalator\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n ethylbenzene:\n name: ethylbenzene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of ethylbenzene in the sample\n title: ethylbenzene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ethylbenzene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000155\n alias: ethylbenzene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n exp_duct:\n name: exp_duct\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The amount of exposed ductwork in the room\n title: exposed ductwork\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exposed ductwork\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000144\n alias: exp_duct\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n exp_pipe:\n name: exp_pipe\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of exposed pipes in the room\n title: exposed pipes\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exposed pipes\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000220\n alias: exp_pipe\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n experimental_factor:\n name: experimental_factor\n annotations:\n expected_value:\n tag: expected_value\n value: text or EFO and/or OBI\n description: Experimental factors are essentially the variable aspects of an experiment\n design which can be used to describe an experiment, or set of experiments, in\n an increasingly detailed manner. This field accepts ontology terms from Experimental\n Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For\n a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\n title: experimental factor\n examples:\n - value: time series design [EFO:EFO_0001779]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - experimental factor\n rank: 1000\n is_a: investigation field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000008\n alias: experimental_factor\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n ext_door:\n name: ext_door\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of exterior doors in the built structure\n title: exterior door count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - exterior door count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000170\n alias: ext_door\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n ext_wall_orient:\n name: ext_wall_orient\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The orientation of the exterior wall\n title: orientations of exterior wall\n examples:\n - value: northwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - orientations of exterior wall\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000817\n alias: ext_wall_orient\n owner: Biosample\n domain_of:\n - Biosample\n range: ext_wall_orient_enum\n multivalued: false\n ext_window_orient:\n name: ext_window_orient\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The compass direction the exterior window of the room is facing\n title: orientations of exterior window\n examples:\n - value: southwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - orientations of exterior window\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000818\n alias: ext_window_orient\n owner: Biosample\n domain_of:\n - Biosample\n range: ext_window_orient_enum\n multivalued: false\n extreme_event:\n name: extreme_event\n annotations:\n expected_value:\n tag: expected_value\n value: date, string\n description: Unusual physical events that may have affected microbial populations\n title: history/extreme events\n examples:\n - value: 1980-05-18, volcanic eruption\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/extreme events\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000320\n alias: extreme_event\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n fao_class:\n name: fao_class\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification from the FAO World Reference Database for Soil\n Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\n title: soil_taxonomic/FAO classification\n examples:\n - value: Luvisols\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/FAO classification\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001083\n alias: fao_class\n owner: Biosample\n domain_of:\n - Biosample\n range: fao_class_enum\n multivalued: false\n fertilizer_regm:\n name: fertilizer_regm\n annotations:\n expected_value:\n tag: expected_value\n value: fertilizer name;fertilizer amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the use of fertilizers; should\n include the name of fertilizer, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple fertilizer\n regimens\n title: fertilizer regimen\n examples:\n - value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fertilizer regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000556\n alias: fertilizer_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n field:\n name: field\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the hydrocarbon field (e.g. Albacora)\n title: field name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - field name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000291\n alias: field\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n filter_type:\n name: filter_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: A device which removes solid particulates or airborne molecular contaminants\n title: filter type\n examples:\n - value: HEPA\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - filter type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000765\n alias: filter_type\n owner: Biosample\n domain_of:\n - Biosample\n range: filter_type_enum\n multivalued: true\n fire:\n name: fire\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n description: Historical and/or physical evidence of fire\n title: history/fire\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n comments:\n - Provide the date the fire occurred. If extended burning occurred provide the\n date range.\n examples:\n - value: '1871-10-10'\n - value: 1871-10-01 to 1871-10-31\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/fire\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001086\n alias: fire\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n pattern: ^[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?(\\s+to\\s+[12]\\d{3}(?:(?:-(?:0[1-9]|1[0-2]))(?:-(?:0[1-9]|[12]\\d|3[01]))?)?)?$\n fireplace_type:\n name: fireplace_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A firebox with chimney\n title: fireplace type\n examples:\n - value: wood burning\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fireplace type\n rank: 1000\n is_a: core field\n string_serialization: '[gas burning|wood burning]'\n slot_uri: MIXS:0000802\n alias: fireplace_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n flooding:\n name: flooding\n annotations:\n expected_value:\n tag: expected_value\n value: date string\n description: Historical and/or physical evidence of flooding\n title: history/flooding\n todos:\n - is \"to\" acceptable? Is there a better way to request that be written?\n - What about if the \"day\" isn't known? Is this ok?\n comments:\n - Provide the date the flood occurred. If extended flooding occurred provide the\n date range.\n examples:\n - value: '1927-04-15'\n - value: 1927-04 to 1927-05\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/flooding\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000319\n alias: flooding\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n floor_age:\n name: floor_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: years, weeks, days\n occurrence:\n tag: occurrence\n value: '1'\n description: The time period since installment of the carpet or flooring\n title: floor age\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000164\n alias: floor_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n floor_area:\n name: floor_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The area of the floor space within the room\n title: floor area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000165\n alias: floor_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n floor_cond:\n name: floor_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the floor at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: floor condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000803\n alias: floor_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_cond_enum\n multivalued: false\n floor_count:\n name: floor_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of floors in the building, including basements and mechanical\n penthouse\n title: floor count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000225\n alias: floor_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n floor_finish_mat:\n name: floor_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The floor covering type; the finished surface that is walked on\n title: floor finish material\n examples:\n - value: carpet\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000804\n alias: floor_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_finish_mat_enum\n multivalued: false\n floor_struc:\n name: floor_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the structural elements and subfloor upon which the finish\n flooring is installed\n title: floor structure\n examples:\n - value: concrete\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000806\n alias: floor_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_struc_enum\n multivalued: false\n floor_thermal_mass:\n name: floor_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the floor to provide inertia against temperature fluctuations\n title: floor thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000166\n alias: floor_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n floor_water_mold:\n name: floor_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew in a room\n title: floor signs of water/mold\n examples:\n - value: ceiling discoloration\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - floor signs of water/mold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000805\n alias: floor_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: floor_water_mold_enum\n multivalued: false\n fluor:\n name: fluor\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram chlorophyll a per cubic meter, volts\n occurrence:\n tag: occurrence\n value: '1'\n description: Raw or converted fluorescence of water\n title: fluorescence\n examples:\n - value: 2.5 volts\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fluorescence\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000704\n alias: fluor\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n freq_clean:\n name: freq_clean\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration or {text}\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times the sample location is cleaned. Frequency of\n cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\n title: frequency of cleaning\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - frequency of cleaning\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000226\n alias: freq_clean\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n freq_cook:\n name: freq_cook\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times a meal is cooked per week\n title: frequency of cooking\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - frequency of cooking\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000227\n alias: freq_cook\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n fungicide_regm:\n name: fungicide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: fungicide name;fungicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of fungicides; should include\n the name of fungicide, amount administered, treatment regimen including how\n many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple fungicide regimens\n title: fungicide regimen\n examples:\n - value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - fungicide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000557\n alias: fungicide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n furniture:\n name: furniture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The types of furniture present in the sampled room\n title: furniture\n examples:\n - value: chair\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - furniture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000807\n alias: furniture\n owner: Biosample\n domain_of:\n - Biosample\n range: furniture_enum\n multivalued: false\n gaseous_environment:\n name: gaseous_environment\n annotations:\n expected_value:\n tag: expected_value\n value: gaseous compound name;gaseous compound amount;treatment interval and\n duration\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Use of conditions with differing gaseous environments; should include\n the name of gaseous compound, amount administered, treatment duration, interval\n and total experimental duration; can include multiple gaseous environment regimens\n title: gaseous environment\n todos:\n - would like to see usage examples for this slot. Requiring micromole/L seems\n too limiting and doesn't match expected_value value\n - did I do this right? keep the example that's provided and add another? so as\n to not override\n examples:\n - value: CO2; 500ppm above ambient; constant\n - value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gaseous environment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000558\n alias: gaseous_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n gaseous_substances:\n name: gaseous_substances\n annotations:\n expected_value:\n tag: expected_value\n value: gaseous substance name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Amount or concentration of substances such as hydrogen sulfide, carbon\n dioxide, methane, etc.; can include multiple substances\n title: gaseous substances\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gaseous substances\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000661\n alias: gaseous_substances\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n gender_restroom:\n name: gender_restroom\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The gender type of the restroom\n title: gender of restroom\n examples:\n - value: male\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gender of restroom\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000808\n alias: gender_restroom\n owner: Biosample\n domain_of:\n - Biosample\n range: gender_restroom_enum\n multivalued: false\n genetic_mod:\n name: genetic_mod\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Genetic modifications of the genome of an organism, which may occur\n naturally by spontaneous mutation, or be introduced by some experimental means,\n e.g. specification of a transgene or the gene knocked-out or details of transient\n transfection\n title: genetic modification\n examples:\n - value: aox1A transgenic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - genetic modification\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0000859\n alias: genetic_mod\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n geo_loc_name:\n name: geo_loc_name\n annotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n name'\n description: The geographical origin of the sample as defined by the country or\n sea name followed by specific region name. Country or sea names should be chosen\n from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n (http://purl.bioontology.org/ontology/GAZ)\n title: geographic location (country and/or sea,region)\n examples:\n - value: 'USA: Maryland, Bethesda'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (country and/or sea,region)\n rank: 1000\n is_a: environment field\n string_serialization: '{term}: {term}, {text}'\n slot_uri: MIXS:0000010\n alias: geo_loc_name\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n glucosidase_act:\n name: glucosidase_act\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mol per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of glucosidase activity\n title: glucosidase activity\n examples:\n - value: 5 mol per liter per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - glucosidase activity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000137\n alias: glucosidase_act\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n gravidity:\n name: gravidity\n annotations:\n expected_value:\n tag: expected_value\n value: gravidity status;timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Whether or not subject is gravid, and if yes date due or date post-conception,\n specifying which is used\n title: gravidity\n examples:\n - value: yes;due date:2018-05-11\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gravidity\n rank: 1000\n is_a: core field\n string_serialization: '{boolean};{timestamp}'\n slot_uri: MIXS:0000875\n alias: gravidity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n gravity:\n name: gravity\n annotations:\n expected_value:\n tag: expected_value\n value: gravity factor value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter per square second, g\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of gravity factor to study\n various types of responses in presence, absence or modified levels of gravity;\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple treatments\n title: gravity\n examples:\n - value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - gravity\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000559\n alias: gravity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n growth_facil:\n name: growth_facil\n annotations:\n expected_value:\n tag: expected_value\n value: free text or CO\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\n title: growth facility\n examples:\n - value: Growth chamber [CO_715:0000189]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth facility\n rank: 1000\n is_a: core field\n string_serialization: '{text}|{termLabel} {[termID]}'\n slot_uri: MIXS:0001043\n alias: growth_facil\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n growth_habit:\n name: growth_habit\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Characteristic shape, appearance or growth form of a plant species\n title: growth habit\n examples:\n - value: spreading\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth habit\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001044\n alias: growth_habit\n owner: Biosample\n domain_of:\n - Biosample\n range: growth_habit_enum\n multivalued: false\n growth_hormone_regm:\n name: growth_hormone_regm\n annotations:\n expected_value:\n tag: expected_value\n value: growth hormone name;growth hormone amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of growth hormones; should\n include the name of growth hormone, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple growth\n hormone regimens\n title: growth hormone regimen\n examples:\n - value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - growth hormone regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000560\n alias: growth_hormone_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n hall_count:\n name: hall_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The total count of hallways and cooridors in the built structure\n title: hallway/corridor count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hallway/corridor count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000228\n alias: hall_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n handidness:\n name: handidness\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The handidness of the individual sampled\n title: handidness\n examples:\n - value: right handedness\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - handidness\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000809\n alias: handidness\n owner: Biosample\n domain_of:\n - Biosample\n range: handidness_enum\n multivalued: false\n hc_produced:\n name: hc_produced\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n etc). If \"other\" is specified, please propose entry in \"additional info\" field\n title: hydrocarbon type produced\n examples:\n - value: Gas\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon type produced\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000989\n alias: hc_produced\n owner: Biosample\n domain_of:\n - Biosample\n range: hc_produced_enum\n multivalued: false\n hcr:\n name: hcr\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR\n defined as a natural environmental feature containing large amounts of hydrocarbons\n at high concentrations potentially suitable for commercial exploitation. This\n term should not be confused with the Hydrocarbon Occurrence term which also\n includes hydrocarbon-rich environments with currently limited commercial interest\n such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose\n entry in \"additional info\" field\n title: hydrocarbon resource type\n examples:\n - value: Oil Sand\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000988\n alias: hcr\n owner: Biosample\n domain_of:\n - Biosample\n range: hcr_enum\n multivalued: false\n hcr_fw_salinity:\n name: hcr_fw_salinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original formation water salinity (prior to secondary recovery e.g.\n Waterflooding) expressed as TDS\n title: formation water salinity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - formation water salinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000406\n alias: hcr_fw_salinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n hcr_geol_age:\n name: hcr_geol_age\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: hydrocarbon resource geological age\n examples:\n - value: Silurian\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource geological age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000993\n alias: hcr_geol_age\n owner: Biosample\n domain_of:\n - Biosample\n range: hcr_geol_age_enum\n multivalued: false\n hcr_pressure:\n name: hcr_pressure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: atmosphere, kilopascal\n occurrence:\n tag: occurrence\n value: '1'\n description: Original pressure of the hydrocarbon resource\n title: hydrocarbon resource original pressure\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource original pressure\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000395\n alias: hcr_pressure\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n hcr_temp:\n name: hcr_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Original temperature of the hydrocarbon resource\n title: hydrocarbon resource original temperature\n examples:\n - value: 150-295 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - hydrocarbon resource original temperature\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000393\n alias: hcr_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n heat_cool_type:\n name: heat_cool_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Methods of conditioning or heating a room or building\n title: heating and cooling system type\n examples:\n - value: heat pump\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating and cooling system type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000766\n alias: heat_cool_type\n owner: Biosample\n domain_of:\n - Biosample\n range: heat_cool_type_enum\n multivalued: true\n heat_deliv_loc:\n name: heat_deliv_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The location of heat delivery within the room\n title: heating delivery locations\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating delivery locations\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000810\n alias: heat_deliv_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: heat_deliv_loc_enum\n multivalued: false\n heat_sys_deliv_meth:\n name: heat_sys_deliv_meth\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The method by which the heat is delivered through the system\n title: heating system delivery method\n examples:\n - value: radiant\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating system delivery method\n rank: 1000\n is_a: core field\n string_serialization: '[conductive|radiant]'\n slot_uri: MIXS:0000812\n alias: heat_sys_deliv_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n heat_system_id:\n name: heat_system_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: The heating system identifier\n title: heating system identifier\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - heating system identifier\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000833\n alias: heat_system_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n heavy_metals:\n name: heavy_metals\n annotations:\n expected_value:\n tag: expected_value\n value: heavy metal name;measurement value unit\n preferred_unit:\n tag: preferred_unit\n value: microgram per gram\n occurrence:\n tag: occurrence\n value: m\n description: Heavy metals present in the sample and their concentrations.\n title: heavy metals/ extreme unusual properties\n todos:\n - Example & validation. Can we configure things so that 27% & 27 % & 0.27 will\n validate?\n - I think it's weird the way GSC writes the title. I recommend this change. Thoughts?\n I would argue this isn't an extreme unusual property. It's just a biogeochemical\n measurement.\n comments:\n - For multiple heavy metals and concentrations, separate by ;\n examples:\n - value: mercury 0.09 micrograms per gram\n - value: mercury 0.09 ug/g; chromium 0.03 ug/g\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - extreme_unusual_properties/heavy metals\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000652\n alias: heavy_metals\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n heavy_metals_meth:\n name: heavy_metals_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining heavy metals\n title: heavy metals method/ extreme unusual properties\n comments:\n - Required when heavy metals are provided\n - If different methods are used for multiple metals, indicate the metal and method.\n Separate metals by ;\n examples:\n - value: https://doi.org/10.3390/ijms9040434\n - value: mercury https://doi.org/10.1007/BF01056090; chromium https://doi.org/10.1007/s00216-006-0322-8\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - extreme_unusual_properties/heavy metals method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000343\n alias: heavy_metals_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n height_carper_fiber:\n name: height_carper_fiber\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average carpet fiber height in the indoor environment\n title: height carpet fiber mat\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - height carpet fiber mat\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000167\n alias: height_carper_fiber\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n herbicide_regm:\n name: herbicide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: herbicide name;herbicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of herbicides; information\n about treatment involving use of growth hormones; should include the name of\n herbicide, amount administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include multiple regimens\n title: herbicide regimen\n examples:\n - value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - herbicide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000561\n alias: herbicide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n horizon_meth:\n name: horizon_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the horizon\n title: soil horizon method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil horizon method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000321\n alias: horizon_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_age:\n name: host_age\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year, day, hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Age of host at the time of sampling; relevant scale depends on species\n and study, e.g. Could be seconds for amoebae or centuries for trees\n title: host age\n examples:\n - value: 10 days\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000255\n alias: host_age\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_body_habitat:\n name: host_body_habitat\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Original body habitat where the sample was obtained from\n title: host body habitat\n examples:\n - value: nasopharynx\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body habitat\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000866\n alias: host_body_habitat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_body_product:\n name: host_body_product\n annotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\n description: Substance produced by the body, e.g. Stool, mucus, where the sample\n was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma\n or https://www.ebi.ac.uk/ols/ontologies/uberon\n title: host body product\n examples:\n - value: mucus [UBERON:0000912]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body product\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000888\n alias: host_body_product\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n host_body_site:\n name: host_body_site\n annotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of body site where the sample was obtained from, such as a specific\n organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\n title: host body site\n examples:\n - value: gill [UBERON:0002535]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body site\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000867\n alias: host_body_site\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n host_body_temp:\n name: host_body_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Core body temperature of the host when sample was collected\n title: host body temperature\n examples:\n - value: 15 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host body temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000274\n alias: host_body_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_color:\n name: host_color\n annotations:\n expected_value:\n tag: expected_value\n value: color\n occurrence:\n tag: occurrence\n value: '1'\n description: The color of host\n title: host color\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host color\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000260\n alias: host_color\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_common_name:\n name: host_common_name\n annotations:\n expected_value:\n tag: expected_value\n value: common name\n occurrence:\n tag: occurrence\n value: '1'\n description: Common name of the host.\n title: host common name\n examples:\n - value: human\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host common name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000248\n alias: host_common_name\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_diet:\n name: host_diet\n annotations:\n expected_value:\n tag: expected_value\n value: diet type\n occurrence:\n tag: occurrence\n value: m\n description: Type of diet depending on the host, for animals omnivore, herbivore\n etc., for humans high-fat, meditteranean etc.; can include multiple diet types\n title: host diet\n examples:\n - value: herbivore\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host diet\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000869\n alias: host_diet\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n host_dry_mass:\n name: host_dry_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of dry mass\n title: host dry mass\n examples:\n - value: 500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host dry mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000257\n alias: host_dry_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_family_relation:\n name: host_family_relation\n annotations:\n expected_value:\n tag: expected_value\n value: relationship type;arbitrary identifier\n occurrence:\n tag: occurrence\n value: m\n description: Familial relationships to other hosts in the same study; can include\n multiple relationships\n title: host family relationship\n examples:\n - value: offspring;Mussel25\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host family relationship\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text}'\n slot_uri: MIXS:0000872\n alias: host_family_relation\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n host_genotype:\n name: host_genotype\n annotations:\n expected_value:\n tag: expected_value\n value: genotype\n occurrence:\n tag: occurrence\n value: '1'\n description: Observed genotype\n title: host genotype\n examples:\n - value: C57BL/6\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host genotype\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000365\n alias: host_genotype\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_growth_cond:\n name: host_growth_cond\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Literature reference giving growth conditions of the host\n title: host growth conditions\n examples:\n - value: https://academic.oup.com/icesjms/article/68/2/349/617247\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host growth conditions\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0000871\n alias: host_growth_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_height:\n name: host_height\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The height of subject\n title: host height\n examples:\n - value: 0.1 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host height\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000264\n alias: host_height\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_last_meal:\n name: host_last_meal\n annotations:\n expected_value:\n tag: expected_value\n value: content;duration\n occurrence:\n tag: occurrence\n value: m\n description: Content of last meal and time since feeding; can include multiple\n values\n title: host last meal\n examples:\n - value: corn feed;P2H\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host last meal\n rank: 1000\n is_a: core field\n string_serialization: '{text};{duration}'\n slot_uri: MIXS:0000870\n alias: host_last_meal\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n host_length:\n name: host_length\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The length of subject\n title: host length\n examples:\n - value: 1 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host length\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000256\n alias: host_length\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_life_stage:\n name: host_life_stage\n annotations:\n expected_value:\n tag: expected_value\n value: stage\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of life stage of host\n title: host life stage\n examples:\n - value: adult\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host life stage\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000251\n alias: host_life_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_phenotype:\n name: host_phenotype\n annotations:\n expected_value:\n tag: expected_value\n value: PATO or HP\n occurrence:\n tag: occurrence\n value: '1'\n description: Phenotype of human or other host. For phenotypic quality ontology\n (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.\n For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\n title: host phenotype\n examples:\n - value: elongated [PATO:0001154]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host phenotype\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000874\n alias: host_phenotype\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n host_sex:\n name: host_sex\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Gender or physical sex of the host.\n title: host sex\n examples:\n - value: non-binary\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host sex\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000811\n alias: host_sex\n owner: Biosample\n domain_of:\n - Biosample\n range: host_sex_enum\n multivalued: false\n host_shape:\n name: host_shape\n annotations:\n expected_value:\n tag: expected_value\n value: shape\n occurrence:\n tag: occurrence\n value: '1'\n description: Morphological shape of host\n title: host shape\n examples:\n - value: round\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host shape\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000261\n alias: host_shape\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_subject_id:\n name: host_subject_id\n annotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\n description: A unique identifier by which each subject can be referred to, de-identified.\n title: host subject id\n examples:\n - value: MPI123\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host subject id\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000861\n alias: host_subject_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_subspecf_genlin:\n name: host_subspecf_genlin\n annotations:\n expected_value:\n tag: expected_value\n value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n e.g. serovar, biotype, ecotype, variety, cultivar.\n occurrence:\n tag: occurrence\n value: m\n description: Information about the genetic distinctness of the host organism below\n the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n or any relevant genetic typing schemes like Group I plasmid. Subspecies should\n not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage\n name and the lineage rank separated by a colon, e.g., biovar:abc123.\n title: host subspecific genetic lineage\n examples:\n - value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host subspecific genetic lineage\n rank: 1000\n is_a: core field\n string_serialization: '{rank name}:{text}'\n slot_uri: MIXS:0001318\n alias: host_subspecf_genlin\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n host_substrate:\n name: host_substrate\n annotations:\n expected_value:\n tag: expected_value\n value: substrate name\n occurrence:\n tag: occurrence\n value: '1'\n description: The growth substrate of the host.\n title: host substrate\n examples:\n - value: rock\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host substrate\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000252\n alias: host_substrate\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n host_symbiont:\n name: host_symbiont\n annotations:\n expected_value:\n tag: expected_value\n value: species name or common name\n occurrence:\n tag: occurrence\n value: m\n description: The taxonomic name of the organism(s) found living in mutualistic,\n commensalistic, or parasitic symbiosis with the specific host.\n title: observed host symbionts\n examples:\n - value: flukeworms\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - observed host symbionts\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001298\n alias: host_symbiont\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n host_tot_mass:\n name: host_tot_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Total mass of the host at collection, the unit depends on host\n title: host total mass\n examples:\n - value: 2500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host total mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000263\n alias: host_tot_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n host_wet_mass:\n name: host_wet_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of wet mass\n title: host wet mass\n examples:\n - value: 1500 gram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - host wet mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000567\n alias: host_wet_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n humidity:\n name: humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Amount of water vapour in the air, at the time of sampling\n title: humidity\n examples:\n - value: 25 gram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000100\n alias: humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n humidity_regm:\n name: humidity_regm\n annotations:\n expected_value:\n tag: expected_value\n value: humidity value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to varying degree\n of humidity; information about treatment involving use of growth hormones; should\n include amount of humidity administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple regimens\n title: humidity regimen\n examples:\n - value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - humidity regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000568\n alias: humidity_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n indoor_space:\n name: indoor_space\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: A distinguishable space within a structure, the purpose for which\n discrete areas of a building is used\n title: indoor space\n examples:\n - value: foyer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - indoor space\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000763\n alias: indoor_space\n owner: Biosample\n domain_of:\n - Biosample\n range: indoor_space_enum\n multivalued: false\n indoor_surf:\n name: indoor_surf\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Type of indoor surface\n title: indoor surface\n examples:\n - value: wall\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - indoor surface\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000764\n alias: indoor_surf\n owner: Biosample\n domain_of:\n - Biosample\n range: indoor_surf_enum\n multivalued: false\n indust_eff_percent:\n name: indust_eff_percent\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Percentage of industrial effluents received by wastewater treatment\n plant\n title: industrial effluent percent\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - industrial effluent percent\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000662\n alias: indust_eff_percent\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n inorg_particles:\n name: inorg_particles\n annotations:\n expected_value:\n tag: expected_value\n value: inorganic particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of particles such as sand, grit, metal particles, ceramics,\n etc.; can include multiple particles\n title: inorganic particles\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - inorganic particles\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000664\n alias: inorg_particles\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n inside_lux:\n name: inside_lux\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatt per square metre\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded value at sampling time (power density)\n title: inside lux light\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - inside lux light\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000168\n alias: inside_lux\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n int_wall_cond:\n name: int_wall_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the wall at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\n title: interior wall condition\n examples:\n - value: damaged\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - interior wall condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000813\n alias: int_wall_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: int_wall_cond_enum\n multivalued: false\n investigation field:\n name: investigation field\n description: field describing aspect of the investigation/study to which the sample\n belongs\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: investigation_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n iw_bt_date_well:\n name: iw_bt_date_well\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Injection water breakthrough date per well following a secondary\n and/or tertiary recovery\n title: injection water breakthrough date of specific well\n examples:\n - value: '2018-05-11'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - injection water breakthrough date of specific well\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001010\n alias: iw_bt_date_well\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n iwf:\n name: iwf\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: Proportion of the produced fluids derived from injected water at\n the time of sampling. (e.g. 87%)\n title: injection water fraction\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - injection water fraction\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000455\n alias: iwf\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n last_clean:\n name: last_clean\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: The last time the floor was cleaned (swept, mopped, vacuumed)\n title: last time swept/mopped/vacuumed\n examples:\n - value: 2018-05-11:T14:30Z\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - last time swept/mopped/vacuumed\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000814\n alias: last_clean\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n lat_lon:\n name: lat_lon\n annotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\n description: The geographical origin of the sample as defined by latitude and\n longitude. The values should be reported in decimal degrees and in WGS84 system\n title: geographic location (latitude and longitude)\n notes:\n - This is currently a required field but it's not clear if this should be required\n for human hosts\n examples:\n - value: 50.586825 6.408977\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (latitude and longitude)\n rank: 1000\n is_a: environment field\n string_serialization: '{float} {float}'\n slot_uri: MIXS:0000009\n alias: lat_lon\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: GeolocationValue\n multivalued: false\n lbc_thirty:\n name: lbc_thirty\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\n description: lime buffer capacity, determined after 30 minute incubation\n title: lime buffer capacity (at 30 minutes)\n comments:\n - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n one pH unit\n examples:\n - value: 543 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n - https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\n aliases:\n - lbc_thirty\n - lbc30\n - lime buffer capacity (at 30 minutes)\n rank: 1000\n alias: lbc_thirty\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n lbceq:\n name: lbceq\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\n description: lime buffer capacity, determined at equilibrium after 5 day incubation\n title: lime buffer capacity (after 5 day incubation)\n comments:\n - This is the mass of lime, in mg, needed to raise the pH of one kg of soil by\n one pH unit\n examples:\n - value: 1575 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - lbceq\n - lime buffer capacity (at 5-day equilibrium)\n rank: 1000\n alias: lbceq\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n light_intensity:\n name: light_intensity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of light intensity\n title: light intensity\n examples:\n - value: 0.3 lux\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light intensity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000706\n alias: light_intensity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n light_regm:\n name: light_regm\n annotations:\n expected_value:\n tag: expected_value\n value: exposure type;light intensity;light quality\n preferred_unit:\n tag: preferred_unit\n value: lux; micrometer, nanometer, angstrom\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about treatment(s) involving exposure to light, including\n both light intensity and quality.\n title: light regimen\n examples:\n - value: incandescant light;10 lux;450 nanometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000569\n alias: light_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n light_type:\n name: light_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Application of light to achieve some practical or aesthetic effect.\n Lighting includes the use of both artificial light sources such as lamps and\n light fixtures, as well as natural illumination by capturing daylight. Can also\n include absence of light\n title: light type\n examples:\n - value: desk lamp\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - light type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000769\n alias: light_type\n owner: Biosample\n domain_of:\n - Biosample\n range: light_type_enum\n multivalued: true\n link_addit_analys:\n name: link_addit_analys\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to additional analysis results performed on the sample\n title: links to additional analysis\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - links to additional analysis\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000340\n alias: link_addit_analys\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n link_class_info:\n name: link_class_info\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to digitized soil maps or other soil classification information\n title: link to classification information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - link to classification information\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000329\n alias: link_class_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n link_climate_info:\n name: link_climate_info\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Link to climate resource\n title: link to climate information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - link to climate information\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000328\n alias: link_climate_info\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n lithology:\n name: lithology\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: lithology\n examples:\n - value: Volcanic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - lithology\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000990\n alias: lithology\n owner: Biosample\n domain_of:\n - Biosample\n range: lithology_enum\n multivalued: false\n local_class:\n name: local_class\n annotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification based on local soil classification system\n title: soil_taxonomic/local classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000330\n alias: local_class\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n local_class_meth:\n name: local_class_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the local soil classification\n title: soil_taxonomic/local classification method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000331\n alias: local_class_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n magnesium:\n name: magnesium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter, parts per million, micromole per\n kilogram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of magnesium in the sample\n title: magnesium\n examples:\n - value: 52.8 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - magnesium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000431\n alias: magnesium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n manganese:\n name: manganese\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of manganese in the sample\n title: manganese\n examples:\n - value: 24.7 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - manganese\n rank: 1000\n alias: manganese\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n max_occup:\n name: max_occup\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The maximum amount of people allowed in the indoor environment\n title: maximum occupancy\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - maximum occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000229\n alias: max_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n mean_frict_vel:\n name: mean_frict_vel\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of mean friction velocity\n title: mean friction velocity\n examples:\n - value: 0.5 meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean friction velocity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000498\n alias: mean_frict_vel\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n mean_peak_frict_vel:\n name: mean_peak_frict_vel\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of mean peak friction velocity\n title: mean peak friction velocity\n examples:\n - value: 1 meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean peak friction velocity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000502\n alias: mean_peak_frict_vel\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n mech_struc:\n name: mech_struc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'mechanical structure: a moving structure'\n title: mechanical structure\n examples:\n - value: elevator\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mechanical structure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000815\n alias: mech_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: mech_struc_enum\n multivalued: false\n mechanical_damage:\n name: mechanical_damage\n annotations:\n expected_value:\n tag: expected_value\n value: damage type;body site\n occurrence:\n tag: occurrence\n value: m\n description: Information about any mechanical damage exerted on the plant; can\n include multiple damages and sites\n title: mechanical damage\n examples:\n - value: pruning;bark\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mechanical damage\n rank: 1000\n is_a: core field\n string_serialization: '{text};{text}'\n slot_uri: MIXS:0001052\n alias: mechanical_damage\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n methane:\n name: methane\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per billion, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Methane (gas) amount or concentration at the time of sampling\n title: methane\n examples:\n - value: 1800 parts per billion\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - methane\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000101\n alias: methane\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n micro_biomass_meth:\n name: micro_biomass_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining microbial biomass\n title: microbial biomass method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - microbial biomass method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000339\n alias: micro_biomass_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n microbial_biomass:\n name: microbial_biomass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram per kilogram soil\n occurrence:\n tag: occurrence\n value: '1'\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer. If you keep this, you would need\n to have correction factors used for conversion to the final units\n title: microbial biomass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - microbial biomass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000650\n alias: microbial_biomass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n mineral_nutr_regm:\n name: mineral_nutr_regm\n annotations:\n expected_value:\n tag: expected_value\n value: mineral nutrient name;mineral nutrient amount;treatment interval and\n duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the use of mineral supplements;\n should include the name of mineral nutrient, amount administered, treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n mineral nutrient regimens\n title: mineral nutrient regimen\n examples:\n - value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mineral nutrient regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000570\n alias: mineral_nutr_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n misc_param:\n name: misc_param\n annotations:\n expected_value:\n tag: expected_value\n value: parameter name;measurement value\n occurrence:\n tag: occurrence\n value: m\n description: Any other measurement performed or parameter collected, that is not\n listed here\n title: miscellaneous parameter\n examples:\n - value: Bicarbonate ion concentration;2075 micromole per kilogram\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - miscellaneous parameter\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000752\n alias: misc_param\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n n_alkanes:\n name: n_alkanes\n annotations:\n expected_value:\n tag: expected_value\n value: n-alkane name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of n-alkanes; can include multiple n-alkanes\n title: n-alkanes\n examples:\n - value: n-hexadecane;100 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - n-alkanes\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000503\n alias: n_alkanes\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n nitrate:\n name: nitrate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrate in the sample\n title: nitrate\n examples:\n - value: 65 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000425\n alias: nitrate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n nitrate_nitrogen:\n name: nitrate_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrate nitrogen in the sample\n title: nitrate_nitrogen\n comments:\n - often below some specified limit of detection\n examples:\n - value: 0.29 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - nitrate_nitrogen\n - NO3-N\n rank: 1000\n alias: nitrate_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitrite:\n name: nitrite\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrite in the sample\n title: nitrite\n examples:\n - value: 0.5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrite\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000426\n alias: nitrite\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n nitrite_nitrogen:\n name: nitrite_nitrogen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrite nitrogen in the sample\n title: nitrite_nitrogen\n examples:\n - value: 1.2 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - nitrite_nitrogen\n - NO2-N\n rank: 1000\n alias: nitrite_nitrogen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n nitro:\n name: nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of nitrogen (total)\n title: nitrogen\n examples:\n - value: 4.2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000504\n alias: nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n non_min_nutr_regm:\n name: non_min_nutr_regm\n annotations:\n expected_value:\n tag: expected_value\n value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving the exposure of plant to non-mineral\n nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n nutrient, amount administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end\n time of the entire treatment; can include multiple non-mineral nutrient regimens\n title: non-mineral nutrient regimen\n examples:\n - value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - non-mineral nutrient regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000571\n alias: non_min_nutr_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n nucleic acid sequence source field:\n name: nucleic acid sequence source field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: nucleic_acid_sequence_source_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n number_pets:\n name: number_pets\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of pets residing in the sampled space\n title: number of pets\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of pets\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000231\n alias: number_pets\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n number_plants:\n name: number_plants\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of plant(s) in the sampling space\n title: number of houseplants\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of houseplants\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000230\n alias: number_plants\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n number_resident:\n name: number_resident\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of individuals currently occupying in the sampling location\n title: number of residents\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - number of residents\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000232\n alias: number_resident\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n occup_density_samp:\n name: occup_density_samp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Average number of occupants at time of sampling per square footage\n title: occupant density at sampling\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupant density at sampling\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000217\n alias: occup_density_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n occup_document:\n name: occup_document\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of documentation of occupancy\n title: occupancy documentation\n examples:\n - value: estimate\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupancy documentation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000816\n alias: occup_document\n owner: Biosample\n domain_of:\n - Biosample\n range: occup_document_enum\n multivalued: false\n occup_samp:\n name: occup_samp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Number of occupants present at time of sample within the given space\n title: occupancy at sampling\n examples:\n - value: '10'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - occupancy at sampling\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000772\n alias: occup_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n org_carb:\n name: org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic carbon\n title: organic carbon\n examples:\n - value: 1.5 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000508\n alias: org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n org_count_qpcr_info:\n name: org_count_qpcr_info\n annotations:\n expected_value:\n tag: expected_value\n value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles\n preferred_unit:\n tag: preferred_unit\n value: number of cells per gram (or ml or cm^2)\n occurrence:\n tag: occurrence\n value: '1'\n description: 'If qpcr was used for the cell count, the target gene name, the primer\n sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n 30 cycles)'\n title: organism count qPCR information\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organism count qPCR information\n rank: 1000\n is_a: core field\n string_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles'\n slot_uri: MIXS:0000099\n alias: org_count_qpcr_info\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n org_matter:\n name: org_matter\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic matter\n title: organic matter\n examples:\n - value: 1.75 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic matter\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000204\n alias: org_matter\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n org_nitro:\n name: org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of organic nitrogen\n title: organic nitrogen\n examples:\n - value: 4 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000205\n alias: org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n org_particles:\n name: org_particles\n annotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of particles such as faeces, hairs, food, vomit, paper\n fibers, plant material, humus, etc.\n title: organic particles\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organic particles\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000665\n alias: org_particles\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n organism_count:\n name: organism_count\n annotations:\n expected_value:\n tag: expected_value\n value: organism name;measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: number of cells per cubic meter, number of cells per milliliter, number\n of cells per cubic centimeter\n occurrence:\n tag: occurrence\n value: m\n description: 'Total cell count of any organism (or group of organisms) per gram,\n volume or area of sample, should include name of organism followed by count.\n The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should\n also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\n title: organism count\n examples:\n - value: total prokaryotes;3.5e7 cells per milliliter;qPCR\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - organism count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000103\n alias: organism_count\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n owc_tvdss:\n name: owc_tvdss\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\n title: oil water contact depth\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oil water contact depth\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000405\n alias: owc_tvdss\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n oxy_stat_samp:\n name: oxy_stat_samp\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Oxygenation status of sample\n title: oxygenation status of sample\n examples:\n - value: aerobic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oxygenation status of sample\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000753\n alias: oxy_stat_samp\n owner: Biosample\n domain_of:\n - Biosample\n range: oxy_stat_samp_enum\n multivalued: false\n oxygen:\n name: oxygen\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Oxygen (gas) amount or concentration at the time of sampling\n title: oxygen\n examples:\n - value: 600 parts per million\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - oxygen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000104\n alias: oxygen\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n part_org_carb:\n name: part_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of particulate organic carbon\n title: particulate organic carbon\n examples:\n - value: 1.92 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particulate organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000515\n alias: part_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n part_org_nitro:\n name: part_org_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of particulate organic nitrogen\n title: particulate organic nitrogen\n examples:\n - value: 0.3 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particulate organic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000719\n alias: part_org_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n particle_class:\n name: particle_class\n annotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: m\n description: Particles are classified, based on their size, into six general categories:clay,\n silt, sand, gravel, cobbles, and boulders; should include amount of particle\n preceded by the name of the particle type; can include multiple values\n title: particle classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - particle classification\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000206\n alias: particle_class\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n permeability:\n name: permeability\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: mD\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Measure of the ability of a hydrocarbon resource to allow fluids\n to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\n title: permeability\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - permeability\n rank: 1000\n is_a: core field\n string_serialization: '{integer} - {integer} {unit}'\n slot_uri: MIXS:0000404\n alias: permeability\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n perturbation:\n name: perturbation\n annotations:\n expected_value:\n tag: expected_value\n value: perturbation type name;perturbation interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Type of perturbation, e.g. chemical administration, physical disturbance,\n etc., coupled with perturbation regimen including how many times the perturbation\n was repeated, how long each perturbation lasted, and the start and end time\n of the entire perturbation period; can include multiple perturbation types\n title: perturbation\n examples:\n - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - perturbation\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000754\n alias: perturbation\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n pesticide_regm:\n name: pesticide_regm\n annotations:\n expected_value:\n tag: expected_value\n value: pesticide name;pesticide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of insecticides; should\n include the name of pesticide, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple pesticide\n regimens\n title: pesticide regimen\n examples:\n - value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pesticide regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000573\n alias: pesticide_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n petroleum_hydrocarb:\n name: petroleum_hydrocarb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of petroleum hydrocarbon\n title: petroleum hydrocarbon\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - petroleum hydrocarbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000516\n alias: petroleum_hydrocarb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ph:\n name: ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Ph measurement of the sample, or liquid portion of sample, or aqueous\n phase of the fluid\n title: pH\n examples:\n - value: '7.2'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001001\n alias: ph\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n multivalued: false\n ph_meth:\n name: ph_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining ph\n title: pH method\n comments:\n - This can include a link to the instrument used or a citation for the method.\n examples:\n - value: https://www.southernlabware.com/pc9500-benchtop-ph-conductivity-meter-kit-ph-accuracy-2000mv-ph-range-2-000-to-20-000.html?gclid=Cj0KCQiAwJWdBhCYARIsAJc4idCO5vtvbVMf545fcvdROFqa6zjzNSoywNx6K4k9Coo9cCc2pybtvGsaAiR0EALw_wcB\n - value: https://doi.org/10.2136/sssabookser5.3.c16\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0001106\n alias: ph_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n ph_regm:\n name: ph_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving exposure of plants to varying\n levels of ph of the growth media, treatment regimen including how many times\n the treatment was repeated, how long each treatment lasted, and the start and\n end time of the entire treatment; can include multiple regimen\n title: pH regimen\n examples:\n - value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pH regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001056\n alias: ph_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n phaeopigments:\n name: phaeopigments\n annotations:\n expected_value:\n tag: expected_value\n value: phaeopigment name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of phaeopigments; can include multiple phaeopigments\n title: phaeopigments\n examples:\n - value: 2.5 milligram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phaeopigments\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000180\n alias: phaeopigments\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n phosphate:\n name: phosphate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of phosphate\n title: phosphate\n examples:\n - value: 0.7 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phosphate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000505\n alias: phosphate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n phosplipid_fatt_acid:\n name: phosplipid_fatt_acid\n annotations:\n expected_value:\n tag: expected_value\n value: phospholipid fatty acid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per gram, mole per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of phospholipid fatty acids; can include multiple values\n title: phospholipid fatty acid\n examples:\n - value: 2.98 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - phospholipid fatty acid\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000181\n alias: phosplipid_fatt_acid\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n photon_flux:\n name: photon_flux\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: number of photons per second per unit area\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of photon flux\n title: photon flux\n examples:\n - value: 3.926 micromole photons per second per square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - photon flux\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000725\n alias: photon_flux\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n plant_growth_med:\n name: plant_growth_med\n annotations:\n expected_value:\n tag: expected_value\n value: EO or enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Specification of the media for growing the plants or tissue cultured\n samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in\n vitro liquid culture medium. Recommended value is a specific value from EO:plant\n growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)\n or other controlled vocabulary\n title: plant growth medium\n examples:\n - value: hydroponic plant culture media [EO:0007067]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant growth medium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001057\n alias: plant_growth_med\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n plant_product:\n name: plant_product\n annotations:\n expected_value:\n tag: expected_value\n value: product name\n occurrence:\n tag: occurrence\n value: '1'\n description: Substance produced by the plant, where the sample was obtained from\n title: plant product\n examples:\n - value: xylem sap [PO:0025539]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant product\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001058\n alias: plant_product\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n plant_sex:\n name: plant_sex\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Sex of the reproductive parts on the whole plant, e.g. pistillate,\n staminate, monoecieous, hermaphrodite.\n title: plant sex\n examples:\n - value: Hermaphroditic\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant sex\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001059\n alias: plant_sex\n owner: Biosample\n domain_of:\n - Biosample\n range: plant_sex_enum\n multivalued: false\n plant_struc:\n name: plant_struc\n annotations:\n expected_value:\n tag: expected_value\n value: PO\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of plant structure the sample was obtained from; for Plant Ontology\n (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the\n sex of it can be recorded here.\n title: plant structure\n examples:\n - value: epidermis [PO:0005679]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - plant structure\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0001060\n alias: plant_struc\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n pollutants:\n name: pollutants\n annotations:\n expected_value:\n tag: expected_value\n value: pollutant name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter, microgram per cubic meter\n occurrence:\n tag: occurrence\n value: m\n description: Pollutant types and, amount or concentrations measured at the time\n of sampling; can report multiple pollutants by entering numeric values preceded\n by name of pollutant\n title: pollutants\n examples:\n - value: lead;0.15 microgram per cubic meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pollutants\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000107\n alias: pollutants\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n porosity:\n name: porosity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value or range\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Porosity of deposited sediment is volume of voids divided by the\n total volume of sample\n title: porosity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - porosity\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000211\n alias: porosity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n potassium:\n name: potassium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of potassium in the sample\n title: potassium\n examples:\n - value: 463 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - potassium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000430\n alias: potassium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n pour_point:\n name: pour_point\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Temperature at which a liquid becomes semi solid and loses its flow\n characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with\n a high paraffin content, typically found in crude deriving from a larger proportion\n of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\n title: pour point\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pour point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000127\n alias: pour_point\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n pre_treatment:\n name: pre_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: pre-treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process of pre-treatment removes materials that can be easily\n collected from the raw wastewater\n title: pre-treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pre-treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000348\n alias: pre_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n pres_animal_insect:\n name: pres_animal_insect\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration;count\n occurrence:\n tag: occurrence\n value: '1'\n description: The type and number of animals or insects present in the sampling\n space.\n title: presence of pets, animals, or insects\n examples:\n - value: cat;5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - presence of pets, animals, or insects\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000819\n alias: pres_animal_insect\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n pattern: ^(cat|dog|rodent|snake|other);\\d+$\n pressure:\n name: pressure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: atmosphere\n occurrence:\n tag: occurrence\n value: '1'\n description: Pressure to which the sample is subject to, in atmospheres\n title: pressure\n examples:\n - value: 50 atmosphere\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000412\n alias: pressure\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n prev_land_use_meth:\n name: prev_land_use_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining previous land use and dates\n title: history/previous land use method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/previous land use method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000316\n alias: prev_land_use_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n previous_land_use:\n name: previous_land_use\n annotations:\n expected_value:\n tag: expected_value\n value: land use name;date\n occurrence:\n tag: occurrence\n value: '1'\n description: Previous land use and dates\n title: history/previous land use\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/previous land use\n rank: 1000\n is_a: core field\n string_serialization: '{text};{timestamp}'\n slot_uri: MIXS:0000315\n alias: previous_land_use\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n primary_prod:\n name: primary_prod\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, gram per square meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of primary production, generally measured as isotope\n uptake\n title: primary production\n examples:\n - value: 100 milligram per cubic meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - primary production\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000728\n alias: primary_prod\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n primary_treatment:\n name: primary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: primary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process to produce both a generally homogeneous liquid capable\n of being treated biologically and a sludge that can be separately treated or\n processed\n title: primary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - primary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000349\n alias: primary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n prod_rate:\n name: prod_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Oil and/or gas production rates per well (e.g. 524 m3 / day)\n title: production rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - production rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000452\n alias: prod_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n prod_start_date:\n name: prod_start_date\n annotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\n description: Date of field's first production\n title: production start date\n examples:\n - value: '2018-05-11'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - production start date\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001008\n alias: prod_start_date\n owner: Biosample\n domain_of:\n - Biosample\n range: TimestampValue\n multivalued: false\n profile_position:\n name: profile_position\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Cross-sectional position in the hillslope where sample was collected.sample\n area position in relation to surrounding areas\n title: profile position\n examples:\n - value: summit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - profile position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001084\n alias: profile_position\n owner: Biosample\n domain_of:\n - Biosample\n range: profile_position_enum\n multivalued: false\n quad_pos:\n name: quad_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The quadrant position of the sampling room within the building\n title: quadrant position\n examples:\n - value: West side\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - quadrant position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000820\n alias: quad_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: quad_pos_enum\n multivalued: false\n radiation_regm:\n name: radiation_regm\n annotations:\n expected_value:\n tag: expected_value\n value: radiation type name;radiation amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: rad, gray\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving exposure of plant or a plant\n part to a particular radiation regimen; should include the radiation type, amount\n or intensity administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple radiation regimens\n title: radiation regimen\n examples:\n - value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - radiation regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000575\n alias: radiation_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n rainfall_regm:\n name: rainfall_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to a given amount\n of rainfall, treatment regimen including how many times the treatment was repeated,\n how long each treatment lasted, and the start and end time of the entire treatment;\n can include multiple regimens\n title: rainfall regimen\n examples:\n - value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rainfall regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000576\n alias: rainfall_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n reactor_type:\n name: reactor_type\n annotations:\n expected_value:\n tag: expected_value\n value: reactor type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Anaerobic digesters can be designed and engineered to operate using\n a number of different process configurations, as batch or continuous, mesophilic,\n high solid or low solid, and single stage or multistage\n title: reactor type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - reactor type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000350\n alias: reactor_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n redox_potential:\n name: redox_potential\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millivolt\n occurrence:\n tag: occurrence\n value: '1'\n description: Redox potential, measured relative to a hydrogen cell, indicating\n oxidation or reduction potential\n title: redox potential\n examples:\n - value: 300 millivolt\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - redox potential\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000182\n alias: redox_potential\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n rel_air_humidity:\n name: rel_air_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Partial vapor and air pressure, density of the vapor and air, or\n by the actual mass of the vapor and air\n title: relative air humidity\n examples:\n - value: 80%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - relative air humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000121\n alias: rel_air_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n rel_humidity_out:\n name: rel_humidity_out\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded outside relative humidity value at the time of sampling\n title: outside relative humidity\n examples:\n - value: 12 per kilogram of air\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - outside relative humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000188\n alias: rel_humidity_out\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n rel_samp_loc:\n name: rel_samp_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The sampling location within the train car\n title: relative sampling location\n examples:\n - value: center of car\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - relative sampling location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000821\n alias: rel_samp_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: rel_samp_loc_enum\n multivalued: false\n reservoir:\n name: reservoir\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the reservoir (e.g. Carapebus)\n title: reservoir name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - reservoir name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000303\n alias: reservoir\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n resins_pc:\n name: resins_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: resins wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - resins wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000134\n alias: resins_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_air_exch_rate:\n name: room_air_exch_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: liter per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: The rate at which outside air replaces indoor air in a given space\n title: room air exchange rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room air exchange rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000169\n alias: room_air_exch_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n room_architec_elem:\n name: room_architec_elem\n annotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\n description: The unique details and component parts that, together, form the architecture\n of a distinguisahable space within a built structure\n title: room architectural elements\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room architectural elements\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000233\n alias: room_architec_elem\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n room_condt:\n name: room_condt\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The condition of the room at the time of sampling\n title: room condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000822\n alias: room_condt\n owner: Biosample\n domain_of:\n - Biosample\n range: room_condt_enum\n multivalued: false\n room_connected:\n name: room_connected\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: List of rooms connected to the sampling room by a doorway\n title: rooms connected by a doorway\n examples:\n - value: office\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms connected by a doorway\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000826\n alias: room_connected\n owner: Biosample\n domain_of:\n - Biosample\n range: room_connected_enum\n multivalued: false\n room_count:\n name: room_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The total count of rooms in the built structure including all room\n types\n title: room count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000234\n alias: room_count\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_dim:\n name: room_dim\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The length, width and height of sampling room\n title: room dimensions\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room dimensions\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\n slot_uri: MIXS:0000192\n alias: room_dim\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_door_dist:\n name: room_door_dist\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Distance between doors (meters) in the hallway between the sampling\n room and adjacent rooms\n title: room door distance\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room door distance\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000193\n alias: room_door_dist\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_door_share:\n name: room_door_share\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) sharing a door with the\n sampling room\n title: rooms that share a door with sampling room\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that share a door with sampling room\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000242\n alias: room_door_share\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_hallway:\n name: room_hallway\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) located in the same hallway\n as sampling room\n title: rooms that are on the same hallway\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that are on the same hallway\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000238\n alias: room_hallway\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_loc:\n name: room_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The position of the room within the building\n title: room location in building\n examples:\n - value: interior room\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room location in building\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000823\n alias: room_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: room_loc_enum\n multivalued: false\n room_moist_dam_hist:\n name: room_moist_dam_hist\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The history of moisture damage or mold in the past 12 months. Number\n of events of moisture damage or mold observed\n title: room moisture damage or mold history\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room moisture damage or mold history\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000235\n alias: room_moist_dam_hist\n owner: Biosample\n domain_of:\n - Biosample\n range: integer\n multivalued: false\n room_net_area:\n name: room_net_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square feet, square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The net floor area of sampling room. Net area excludes wall thicknesses\n title: room net area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room net area\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000194\n alias: room_net_area\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_occup:\n name: room_occup\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Count of room occupancy at time of sampling\n title: room occupancy\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room occupancy\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000236\n alias: room_occup\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n room_samp_pos:\n name: room_samp_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The horizontal sampling position in the room relative to architectural\n elements\n title: room sampling position\n examples:\n - value: south corner\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room sampling position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000824\n alias: room_samp_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: room_samp_pos_enum\n multivalued: false\n room_type:\n name: room_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The main purpose or activity of the sampling room. A room is any\n distinguishable space within a structure\n title: room type\n examples:\n - value: bathroom\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000825\n alias: room_type\n owner: Biosample\n domain_of:\n - Biosample\n range: room_type_enum\n multivalued: false\n room_vol:\n name: room_vol\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic feet, cubic meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Volume of sampling room\n title: room volume\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room volume\n rank: 1000\n is_a: core field\n string_serialization: '{integer} {unit}'\n slot_uri: MIXS:0000195\n alias: room_vol\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_wall_share:\n name: room_wall_share\n annotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\n description: List of room(s) (room number, room name) sharing a wall with the\n sampling room\n title: rooms that share a wall with sampling room\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooms that share a wall with sampling room\n rank: 1000\n is_a: core field\n string_serialization: '{text};{integer}'\n slot_uri: MIXS:0000243\n alias: room_wall_share\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n room_window_count:\n name: room_window_count\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Number of windows in the room\n title: room window count\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - room window count\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000237\n alias: room_window_count\n owner: Biosample\n domain_of:\n - Biosample\n range: integer\n multivalued: false\n root_cond:\n name: root_cond\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Relevant rooting conditions such as field plot size, sowing density,\n container dimensions, number of plants per container.\n title: rooting conditions\n examples:\n - value: http://himedialabs.com/TD/PT158.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting conditions\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001061\n alias: root_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_carbon:\n name: root_med_carbon\n annotations:\n expected_value:\n tag: expected_value\n value: carbon source name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Source of organic carbon in the culture rooting medium; e.g. sucrose.\n title: rooting medium carbon\n examples:\n - value: sucrose\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium carbon\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000577\n alias: root_med_carbon\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_macronutr:\n name: root_med_macronutr\n annotations:\n expected_value:\n tag: expected_value\n value: macronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of the culture rooting medium macronutrients (N,P, K,\n Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\n title: rooting medium macronutrients\n examples:\n - value: KH2PO4;170\u00ac\u2020milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium macronutrients\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000578\n alias: root_med_macronutr\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_micronutr:\n name: root_med_micronutr\n annotations:\n expected_value:\n tag: expected_value\n value: micronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of the culture rooting medium micronutrients (Fe, Mn,\n Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\n title: rooting medium micronutrients\n examples:\n - value: H3BO3;6.2\u00ac\u2020milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium micronutrients\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000579\n alias: root_med_micronutr\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_ph:\n name: root_med_ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: pH measurement of the culture rooting medium; e.g. 5.5.\n title: rooting medium pH\n examples:\n - value: '7.5'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001062\n alias: root_med_ph\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n root_med_regl:\n name: root_med_regl\n annotations:\n expected_value:\n tag: expected_value\n value: regulator name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Growth regulators in the culture rooting medium such as cytokinins,\n auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\n title: rooting medium regulators\n examples:\n - value: abscisic acid;0.75 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium regulators\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000581\n alias: root_med_regl\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_solid:\n name: root_med_solid\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Specification of the solidifying agent in the culture rooting medium;\n e.g. agar.\n title: rooting medium solidifier\n examples:\n - value: agar\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium solidifier\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0001063\n alias: root_med_solid\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n root_med_suppl:\n name: root_med_suppl\n annotations:\n expected_value:\n tag: expected_value\n value: supplement name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Organic supplements of the culture rooting medium, such as vitamins,\n amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n (0.5\u00ac\u2020mg/L).\n title: rooting medium organic supplements\n examples:\n - value: nicotinic acid;0.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - rooting medium organic supplements\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000580\n alias: root_med_suppl\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n salinity:\n name: salinity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: practical salinity unit, percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: The total concentration of all dissolved salts in a liquid or solid\n sample. While salinity can be measured by a complete chemical analysis, this\n method is difficult and time consuming. More often, it is instead derived from\n the conductivity measurement. This is known as practical salinity. These derivations\n compare the specific conductance of the sample to a salinity standard such as\n seawater.\n title: salinity\n examples:\n - value: 25 practical salinity unit\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salinity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000183\n alias: salinity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n salinity_meth:\n name: salinity_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining salinity\n title: salinity method\n examples:\n - value: https://doi.org/10.1007/978-1-61779-986-0_28\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salinity method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000341\n alias: salinity_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n salt_regm:\n name: salt_regm\n annotations:\n expected_value:\n tag: expected_value\n value: salt name;salt amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving use of salts as supplement\n to liquid and soil growth media; should include the name of salt, amount administered,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple salt regimens\n title: salt regimen\n examples:\n - value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - salt regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000582\n alias: salt_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n samp_capt_status:\n name: samp_capt_status\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Reason for the sample\n title: sample capture status\n examples:\n - value: farm sample\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample capture status\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000860\n alias: samp_capt_status\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_capt_status_enum\n multivalued: false\n samp_collec_device:\n name: samp_collec_device\n annotations:\n expected_value:\n tag: expected_value\n value: device name\n description: The device used to collect an environmental sample. This field accepts\n terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\n title: sample collection device\n examples:\n - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection device\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{termLabel} {[termID]}|{text}'\n slot_uri: MIXS:0000002\n alias: samp_collec_device\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n samp_collec_method:\n name: samp_collec_method\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url , or text\n description: The method employed for collecting the sample.\n title: sample collection method\n examples:\n - value: swabbing\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection method\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001225\n alias: samp_collec_method\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n samp_collect_point:\n name: samp_collect_point\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Sampling point on the asset were sample was collected (e.g. Wellhead,\n storage tank, separator, etc). If \"other\" is specified, please propose entry\n in \"additional info\" field\n title: sample collection point\n examples:\n - value: well\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample collection point\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001015\n alias: samp_collect_point\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_collect_point_enum\n multivalued: false\n samp_dis_stage:\n name: samp_dis_stage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Stage of the disease at the time of sample collection, e.g. inoculation,\n penetration, infection, growth and reproduction, dissemination of pathogen.\n title: sample disease stage\n examples:\n - value: infection\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample disease stage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000249\n alias: samp_dis_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_dis_stage_enum\n multivalued: false\n samp_floor:\n name: samp_floor\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The floor of the building, where the sampling room is located\n title: sampling floor\n examples:\n - value: 4th floor\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling floor\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000828\n alias: samp_floor\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_floor_enum\n multivalued: false\n samp_loc_corr_rate:\n name: samp_loc_corr_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: millimeter per year\n occurrence:\n tag: occurrence\n value: '1'\n description: Metal corrosion rate is the speed of metal deterioration due to environmental\n conditions. As environmental conditions change corrosion rates change accordingly.\n Therefore, long term corrosion rates are generally more informative than short\n term rates and for that reason they are preferred during reporting. In the case\n of suspected MIC, corrosion rate measurements at the time of sampling might\n provide insights into the involvement of certain microbial community members\n in MIC as well as potential microbial interplays\n title: corrosion rate at sample location\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - corrosion rate at sample location\n rank: 1000\n is_a: core field\n string_serialization: '{float} - {float} {unit}'\n slot_uri: MIXS:0000136\n alias: samp_loc_corr_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_mat_process:\n name: samp_mat_process\n annotations:\n expected_value:\n tag: expected_value\n value: text\n description: A brief description of any processing applied to the sample during\n or after retrieving the sample from environment, or a link to the relevant protocol(s)\n performed.\n title: sample material processing\n examples:\n - value: filtering of seawater, storing samples in ethanol\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample material processing\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{text}'\n slot_uri: MIXS:0000016\n alias: samp_mat_process\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledTermValue\n multivalued: false\n samp_md:\n name: samp_md\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: In non deviated well, measured depth is equal to the true vertical\n depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated\n wells, the MD is the length of trajectory of the borehole measured from the\n same reference or datum. Common datums used are ground level (GL), drilling\n rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: sample measured depth\n examples:\n - value: 1534 meter;MSL\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample measured depth\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000413\n alias: samp_md\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n samp_preserv:\n name: samp_preserv\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliliter\n occurrence:\n tag: occurrence\n value: '1'\n description: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\n title: preservative added to sample\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - preservative added to sample\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000463\n alias: samp_preserv\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_room_id:\n name: samp_room_id\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: Sampling room number. This ID should be consistent with the designations\n on the building floor plans\n title: sampling room ID or name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling room ID or name\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000244\n alias: samp_room_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_size:\n name: samp_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, liter\n description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n sample collected.\n title: amount or size of sample collected\n examples:\n - value: 5 liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - amount or size of sample collected\n rank: 1000\n is_a: nucleic acid sequence source field\n slot_uri: MIXS:0000001\n alias: samp_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n samp_sort_meth:\n name: samp_sort_meth\n annotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: m\n description: Method by which samples are sorted; open face filter collecting total\n suspended particles, prefilter to remove particles larger than X micrometers\n in diameter, where common values of X would be 10 and 2.5 full size sorting\n in a cascade impactor.\n title: sample size sorting method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample size sorting method\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000216\n alias: samp_sort_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n samp_store_dur:\n name: samp_store_dur\n annotations:\n expected_value:\n tag: expected_value\n value: duration\n occurrence:\n tag: occurrence\n value: '1'\n description: Duration for which the sample was stored\n title: sample storage duration\n examples:\n - value: P1Y6M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage duration\n rank: 1000\n is_a: core field\n string_serialization: '{duration}'\n slot_uri: MIXS:0000116\n alias: samp_store_dur\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_store_loc:\n name: samp_store_loc\n annotations:\n expected_value:\n tag: expected_value\n value: location name\n occurrence:\n tag: occurrence\n value: '1'\n description: Location at which sample was stored, usually name of a specific freezer/room\n title: sample storage location\n examples:\n - value: Freezer no:5\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage location\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000755\n alias: samp_store_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_store_temp:\n name: samp_store_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature at which sample was stored, e.g. -80 degree Celsius\n title: sample storage temperature\n examples:\n - value: -80 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample storage temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000110\n alias: samp_store_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n samp_subtype:\n name: samp_subtype\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of sample sub-type. For example if \"sample type\" is \"Produced\n Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified,\n please propose entry in \"additional info\" field\n title: sample subtype\n examples:\n - value: biofilm\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample subtype\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000999\n alias: samp_subtype\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_subtype_enum\n multivalued: false\n samp_taxon_id:\n name: samp_taxon_id\n annotations:\n expected_value:\n tag: expected_value\n value: Taxonomy ID\n description: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa\n sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or\n 'blank sample' for negative controls.\n title: Taxonomy ID of DNA sample\n comments:\n - coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Taxonomy ID of DNA sample\n rank: 1000\n is_a: investigation field\n slot_uri: MIXS:0001320\n alias: samp_taxon_id\n owner: Biosample\n domain_of:\n - Biosample\n range: ControlledIdentifiedTermValue\n multivalued: false\n samp_time_out:\n name: samp_time_out\n annotations:\n expected_value:\n tag: expected_value\n value: time\n preferred_unit:\n tag: preferred_unit\n value: hour\n occurrence:\n tag: occurrence\n value: '1'\n description: The recent and long term history of outside sampling\n title: sampling time outside\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling time outside\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000196\n alias: samp_time_out\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_transport_cond:\n name: samp_transport_cond\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: days;degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Sample transport duration (in days or hrs) and temperature the sample\n was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\n title: sample transport conditions\n examples:\n - value: 5 days;-20 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample transport conditions\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000410\n alias: samp_transport_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_tvdss:\n name: samp_tvdss\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value or measurement value range\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Depth of the sample i.e. The vertical distance between the sea level\n and the sampled position in the subsurface. Depth can be reported as an interval\n for subsurface samples e.g. 1325.75-1362.25 m\n title: sample true vertical depth subsea\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample true vertical depth subsea\n rank: 1000\n is_a: core field\n string_serialization: '{float}-{float} {unit}'\n slot_uri: MIXS:0000409\n alias: samp_tvdss\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_type:\n name: samp_type\n annotations:\n expected_value:\n tag: expected_value\n value: GENEPIO:0001246\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material from which the sample was obtained. For the\n Hydrocarbon package, samples include types like core, rock trimmings, drill\n cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid,\n produced water, injected water, swabs, etc. For the Food Package, samples are\n usually categorized as food, body products or tissues, or environmental material.\n This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\n title: sample type\n examples:\n - value: built environment sample [GENEPIO:0001248]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000998\n alias: samp_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n samp_weather:\n name: samp_weather\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The weather on the sampling day\n title: sampling day weather\n examples:\n - value: foggy\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sampling day weather\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000827\n alias: samp_weather\n owner: Biosample\n domain_of:\n - Biosample\n range: samp_weather_enum\n multivalued: false\n samp_well_name:\n name: samp_well_name\n annotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\n description: Name of the well (e.g. BXA1123) where sample was taken\n title: sample well name\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample well name\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000296\n alias: samp_well_name\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n saturates_pc:\n name: saturates_pc\n annotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis\n method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability\n and polarity. There are three main methods to obtain SARA results. The most\n popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source:\n https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\n title: saturates wt%\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - saturates wt%\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000131\n alias: saturates_pc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n season:\n name: season\n annotations:\n expected_value:\n tag: expected_value\n value: NCIT:C94729\n occurrence:\n tag: occurrence\n value: '1'\n description: The season when sampling occurred. Any of the four periods into which\n the year is divided by the equinoxes and solstices. This field accepts terms\n listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).\n title: season\n examples:\n - value: autumn [NCIT:C94733]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - season\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000829\n alias: season\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n season_environment:\n name: season_environment\n annotations:\n expected_value:\n tag: expected_value\n value: seasonal environment name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to a particular season (e.g. Winter,\n summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment\n title: seasonal environment\n examples:\n - value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - seasonal environment\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001068\n alias: season_environment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n season_precpt:\n name: season_precpt\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average of all seasonal precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\n title: average seasonal precipitation\n todos:\n - check validation & examples. always mm? so value only? Or value + unit\n notes:\n - mean and average are the same thing, but it seems like bad practice to not be\n consistent. Changed mean to average\n comments:\n - Seasons are defined as spring (March, April, May), summer (June, July, August),\n autumn (September, October, November) and winter (December, January, February).\n examples:\n - value: 0.4 inch\n - value: 10.16 mm\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean seasonal precipitation\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000645\n alias: season_precpt\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n season_temp:\n name: season_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Mean seasonal temperature\n title: mean seasonal temperature\n examples:\n - value: 18 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - mean seasonal temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000643\n alias: season_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n season_use:\n name: season_use\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The seasons the space is occupied\n title: seasonal use\n examples:\n - value: Winter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - seasonal use\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000830\n alias: season_use\n owner: Biosample\n domain_of:\n - Biosample\n range: season_use_enum\n multivalued: false\n secondary_treatment:\n name: secondary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: secondary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process for substantially degrading the biological content of\n the sewage\n title: secondary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - secondary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000351\n alias: secondary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n sediment_type:\n name: sediment_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Information about the sediment type based on major constituents\n title: sediment type\n examples:\n - value: biogenous\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sediment type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001078\n alias: sediment_type\n owner: Biosample\n domain_of:\n - Biosample\n range: sediment_type_enum\n multivalued: false\n sequencing field:\n name: sequencing field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n abstract: true\n alias: sequencing_field\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n sewage_type:\n name: sewage_type\n annotations:\n expected_value:\n tag: expected_value\n value: sewage type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Type of wastewater treatment plant as municipial or industrial\n title: sewage type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sewage type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000215\n alias: sewage_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n shad_dev_water_mold:\n name: shad_dev_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the shading device\n title: shading device signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000834\n alias: shad_dev_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n shading_device_cond:\n name: shading_device_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the shading device at the time of sampling\n title: shading device condition\n examples:\n - value: new\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000831\n alias: shading_device_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: shading_device_cond_enum\n multivalued: false\n shading_device_loc:\n name: shading_device_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The location of the shading device in relation to the built structure\n title: shading device location\n examples:\n - value: exterior\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device location\n rank: 1000\n is_a: core field\n string_serialization: '[exterior|interior]'\n slot_uri: MIXS:0000832\n alias: shading_device_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n shading_device_mat:\n name: shading_device_mat\n annotations:\n expected_value:\n tag: expected_value\n value: material name\n occurrence:\n tag: occurrence\n value: '1'\n description: The material the shading device is composed of\n title: shading device material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device material\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000245\n alias: shading_device_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n shading_device_type:\n name: shading_device_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of shading device\n title: shading device type\n examples:\n - value: slatted aluminum awning\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - shading device type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000835\n alias: shading_device_type\n owner: Biosample\n domain_of:\n - Biosample\n range: shading_device_type_enum\n multivalued: false\n sieving:\n name: sieving\n annotations:\n expected_value:\n tag: expected_value\n value: design name and/or size;amount\n occurrence:\n tag: occurrence\n value: '1'\n description: Collection design of pooled samples and/or sieve size and amount\n of sample sieved\n title: composite design/sieving\n todos:\n - check validation and examples\n comments:\n - Describe how samples were composited or sieved.\n - Use 'sample link' to indicate which samples were combined.\n examples:\n - value: combined 2 cores | 4mm sieved\n - value: 4 mm sieved and homogenized\n - value: 50 g | 5 cores | 2 mm sieved\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - composite design/sieving\n rank: 1000\n is_a: core field\n string_serialization: '{{text}|{float} {unit}};{float} {unit}'\n slot_uri: MIXS:0000322\n alias: sieving\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n silicate:\n name: silicate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of silicate\n title: silicate\n examples:\n - value: 0.05 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - silicate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000184\n alias: silicate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n size_frac:\n name: size_frac\n annotations:\n expected_value:\n tag: expected_value\n value: filter size value range\n description: Filtering pore size used in sample preparation\n title: size fraction selected\n examples:\n - value: 0-0.22 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size fraction selected\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{float}-{float} {unit}'\n slot_uri: MIXS:0000017\n alias: size_frac\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n size_frac_low:\n name: size_frac_low\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n Materials larger than the size threshold are excluded from the sample\n title: size-fraction lower threshold\n examples:\n - value: 0.2 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size-fraction lower threshold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000735\n alias: size_frac_low\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n size_frac_up:\n name: size_frac_up\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\n description: Refers to the mesh/pore size used to retain the sample. Materials\n smaller than the size threshold are excluded from the sample\n title: size-fraction upper threshold\n examples:\n - value: 20 micrometer\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - size-fraction upper threshold\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000736\n alias: size_frac_up\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n slope_aspect:\n name: slope_aspect\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree\n occurrence:\n tag: occurrence\n value: '1'\n description: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees). This measure\n provides an indication of sun and wind exposure that will influence soil temperature\n and evapotranspiration.\n title: slope aspect\n comments:\n - Aspect is the orientation of slope, measured clockwise in degrees from 0 to\n 360, where 0 is north-facing, 90 is east-facing, 180 is south-facing, and 270\n is west-facing.\n examples:\n - value: '35'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - slope aspect\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000647\n alias: slope_aspect\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n slope_gradient:\n name: slope_gradient\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: Commonly called 'slope'. The angle between ground surface and a horizontal\n line (in percent). This is the direction that overland water would flow. This\n measure is usually taken with a hand level meter or clinometer\n title: slope gradient\n todos:\n - Slope is a percent. How does the validation work? Check to correct examples\n examples:\n - value: 10%\n - value: 10 %\n - value: '0.10'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - slope gradient\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000646\n alias: slope_gradient\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sludge_retent_time:\n name: sludge_retent_time\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: hours\n occurrence:\n tag: occurrence\n value: '1'\n description: The time activated sludge remains in reactor\n title: sludge retention time\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sludge retention time\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000669\n alias: sludge_retent_time\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sodium:\n name: sodium\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Sodium concentration in the sample\n title: sodium\n examples:\n - value: 10.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sodium\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000428\n alias: sodium\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n soil_horizon:\n name: soil_horizon\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Specific layer in the land area which measures parallel to the soil\n surface and possesses physical characteristics which differ from the layers\n above and beneath\n title: soil horizon\n examples:\n - value: A horizon\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil horizon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001082\n alias: soil_horizon\n owner: Biosample\n domain_of:\n - Biosample\n range: soil_horizon_enum\n multivalued: false\n soil_text_measure:\n name: soil_text_measure\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative proportion of different grain sizes of mineral particles\n in a soil, as described using a standard system; express as % sand (50 um to\n 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty\n clay loam) optional.\n title: soil texture measurement\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil texture measurement\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000335\n alias: soil_text_measure\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n soil_texture_meth:\n name: soil_texture_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining soil texture\n title: soil texture method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil texture method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000336\n alias: soil_texture_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n soil_type:\n name: soil_type\n annotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of the soil type or classification. This field accepts\n terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms\n can be separated by pipes.\n title: soil type\n examples:\n - value: plinthosol [ENVO:00002250]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000332\n alias: soil_type\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n soil_type_meth:\n name: soil_type_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining soil series name or other\n lower-level classification\n title: soil type method\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000334\n alias: soil_type_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n solar_irradiance:\n name: solar_irradiance\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatts per square meter per day, ergs per square centimeter per\n second\n occurrence:\n tag: occurrence\n value: '1'\n description: The amount of solar energy that arrives at a specific area of a surface\n during a specific time interval\n title: solar irradiance\n examples:\n - value: 1.36 kilowatts per square meter per day\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - solar irradiance\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000112\n alias: solar_irradiance\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n soluble_inorg_mat:\n name: soluble_inorg_mat\n annotations:\n expected_value:\n tag: expected_value\n value: soluble inorganic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances such as ammonia, road-salt, sea-salt,\n cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.\n title: soluble inorganic material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble inorganic material\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000672\n alias: soluble_inorg_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n soluble_org_mat:\n name: soluble_org_mat\n annotations:\n expected_value:\n tag: expected_value\n value: soluble organic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances such as urea, fruit sugars, soluble proteins,\n drugs, pharmaceuticals, etc.\n title: soluble organic material\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble organic material\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000673\n alias: soluble_org_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n soluble_react_phosp:\n name: soluble_react_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of soluble reactive phosphorus\n title: soluble reactive phosphorus\n examples:\n - value: 0.1 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soluble reactive phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000738\n alias: soluble_react_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n source_mat_id:\n name: source_mat_id\n annotations:\n expected_value:\n tag: expected_value\n value: 'for cultures of microorganisms: identifiers for two culture collections;\n for other material a unique arbitrary identifer'\n description: A globally unique identifier assigned to the biological sample.\n title: source material identifier\n todos:\n - Currently, the comments say to use UUIDs. However, if we implement assigning\n NMDC identifiers with the minter we dont need to require a GUID. It can be an\n optional field to fill out only if they already have a resolvable ID.\n comments:\n - Identifiers must be prefixed. Possible FAIR prefixes are IGSNs (http://www.geosamples.org/getigsn),\n NCBI biosample accession numbers, ARK identifiers (https://arks.org/). These\n IDs enable linking to derived analytes and subsamples. If you have not assigned\n FAIR identifiers to your samples, you can generate UUIDs (https://www.uuidgenerator.net/).\n examples:\n - value: IGSN:AU1243\n - value: UUID:24f1467a-40f4-11ed-b878-0242ac120002\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source material identifiers\n rank: 1000\n is_a: nucleic acid sequence source field\n string_serialization: '{text}'\n slot_uri: MIXS:0000026\n alias: source_mat_id\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n space_typ_state:\n name: space_typ_state\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Customary or normal state of the space\n title: space typical state\n examples:\n - value: typically occupied\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - space typical state\n rank: 1000\n is_a: core field\n string_serialization: '[typically occupied|typically unoccupied]'\n slot_uri: MIXS:0000770\n alias: space_typ_state\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n specific:\n name: specific\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'The building specifications. If design is chosen, indicate phase:\n conceptual, schematic, design development, construction documents'\n title: specifications\n examples:\n - value: construction\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - specifications\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000836\n alias: specific\n owner: Biosample\n domain_of:\n - Biosample\n range: specific_enum\n multivalued: false\n specific_ecosystem:\n name: specific_ecosystem\n description: Specific ecosystems represent specific features of the environment\n like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n Specific ecosystem is in position 5/5 in a GOLD path.\n comments:\n - Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: specific_ecosystem\n owner: Biosample\n domain_of:\n - Biosample\n - Study\n range: string\n specific_humidity:\n name: specific_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\n description: The mass of water vapour in a unit mass of moist air, usually expressed\n as grams of vapour per kilogram of air, or, in air conditioning, as grains per\n pound.\n title: specific humidity\n examples:\n - value: 15 per kilogram of air\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - specific humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000214\n alias: specific_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sr_dep_env:\n name: sr_dep_env\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: source rock depositional environment\n examples:\n - value: Marine\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock depositional environment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000996\n alias: sr_dep_env\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_dep_env_enum\n multivalued: false\n sr_geol_age:\n name: sr_geol_age\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: source rock geological age\n examples:\n - value: Silurian\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock geological age\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000997\n alias: sr_geol_age\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_geol_age_enum\n multivalued: false\n sr_kerog_type:\n name: sr_kerog_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic\n and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/\n fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris\n (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen).\n If \"other\" is specified, please propose entry in \"additional info\" field'\n title: source rock kerogen type\n examples:\n - value: Type IV\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock kerogen type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000994\n alias: sr_kerog_type\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_kerog_type_enum\n multivalued: false\n sr_lithology:\n name: sr_lithology\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\n title: source rock lithology\n examples:\n - value: Coal\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - source rock lithology\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000995\n alias: sr_lithology\n owner: Biosample\n domain_of:\n - Biosample\n range: sr_lithology_enum\n multivalued: false\n standing_water_regm:\n name: standing_water_regm\n annotations:\n expected_value:\n tag: expected_value\n value: standing water type;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\n description: Treatment involving an exposure to standing water during a plant's\n life span, types can be flood water or standing water, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and\n the start and end time of the entire treatment; can include multiple regimens\n title: standing water regimen\n examples:\n - value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - standing water regimen\n rank: 1000\n is_a: core field\n string_serialization: '{text};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0001069\n alias: standing_water_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n store_cond:\n name: store_cond\n annotations:\n expected_value:\n tag: expected_value\n value: storage condition type;duration\n occurrence:\n tag: occurrence\n value: '1'\n description: Explain how and for how long the soil sample was stored before DNA\n extraction (fresh/frozen/other).\n title: storage conditions\n examples:\n - value: -20 degree Celsius freezer;P2Y10D\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - storage conditions\n rank: 1000\n is_a: core field\n string_serialization: '{text};{duration}'\n slot_uri: MIXS:0000327\n alias: store_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n substructure_type:\n name: substructure_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: The substructure or under building is that largely hidden section\n of the building which is built off the foundations to the ground floor level\n title: substructure type\n examples:\n - value: basement\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - substructure type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000767\n alias: substructure_type\n owner: Biosample\n domain_of:\n - Biosample\n range: substructure_type_enum\n multivalued: true\n sulfate:\n name: sulfate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of sulfate in the sample\n title: sulfate\n examples:\n - value: 5 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000423\n alias: sulfate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sulfate_fw:\n name: sulfate_fw\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original sulfate concentration in the hydrocarbon resource\n title: sulfate in formation water\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfate in formation water\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000407\n alias: sulfate_fw\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n sulfide:\n name: sulfide\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of sulfide in the sample\n title: sulfide\n examples:\n - value: 2 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sulfide\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000424\n alias: sulfide\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n surf_air_cont:\n name: surf_air_cont\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Contaminant identified on surface\n title: surface-air contaminant\n examples:\n - value: radon\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface-air contaminant\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000759\n alias: surf_air_cont\n owner: Biosample\n domain_of:\n - Biosample\n range: surf_air_cont_enum\n multivalued: true\n surf_humidity:\n name: surf_humidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Surfaces: water activity as a function of air and material moisture'\n title: surface humidity\n examples:\n - value: 10%\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface humidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000123\n alias: surf_humidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n surf_material:\n name: surf_material\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Surface materials at the point of sampling\n title: surface material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000758\n alias: surf_material\n owner: Biosample\n domain_of:\n - Biosample\n range: surf_material_enum\n multivalued: false\n surf_moisture:\n name: surf_moisture\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million, gram per cubic meter, gram per square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Water held on a surface\n title: surface moisture\n examples:\n - value: 0.01 gram per square meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface moisture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000128\n alias: surf_moisture\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n surf_moisture_ph:\n name: surf_moisture_ph\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: ph measurement of surface\n title: surface moisture pH\n examples:\n - value: '7'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface moisture pH\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000760\n alias: surf_moisture_ph\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n multivalued: false\n surf_temp:\n name: surf_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: Temperature of the surface at the time of sampling\n title: surface temperature\n examples:\n - value: 15 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - surface temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000125\n alias: surf_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n suspend_part_matter:\n name: suspend_part_matter\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of suspended particulate matter\n title: suspended particulate matter\n examples:\n - value: 0.5 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - suspended particulate matter\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000741\n alias: suspend_part_matter\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n suspend_solids:\n name: suspend_solids\n annotations:\n expected_value:\n tag: expected_value\n value: suspended solid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, milligram per liter, mole per liter, gram per liter,\n part per million\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of substances including a wide variety of material,\n such as silt, decaying plant and animal matter; can include multiple substances\n title: suspended solids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - suspended solids\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000150\n alias: suspend_solids\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n tan:\n name: tan\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\n title: total acid number\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total acid number\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000120\n alias: tan\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n temp:\n name: temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n description: Temperature of the sample at the time of sampling.\n title: temperature\n examples:\n - value: 25 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - temperature\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000113\n alias: temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n temp_out:\n name: temp_out\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The recorded temperature value at sampling time outside\n title: temperature outside house\n examples:\n - value: 5 degree Celsius\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - temperature outside house\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000197\n alias: temp_out\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tertiary_treatment:\n name: tertiary_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: tertiary treatment type\n occurrence:\n tag: occurrence\n value: '1'\n description: The process providing a final treatment stage to raise the effluent\n quality before it is discharged to the receiving environment\n title: tertiary treatment\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tertiary treatment\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000352\n alias: tertiary_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n tidal_stage:\n name: tidal_stage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Stage of tide\n title: tidal stage\n examples:\n - value: high tide\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tidal stage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000750\n alias: tidal_stage\n owner: Biosample\n domain_of:\n - Biosample\n range: tidal_stage_enum\n multivalued: false\n tillage:\n name: tillage\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\n description: Note method(s) used for tilling\n title: history/tillage\n examples:\n - value: chisel\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - history/tillage\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0001081\n alias: tillage\n owner: Biosample\n domain_of:\n - Biosample\n range: tillage_enum\n multivalued: true\n tiss_cult_growth_med:\n name: tiss_cult_growth_med\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of plant tissue culture growth media used\n title: tissue culture growth media\n examples:\n - value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - tissue culture growth media\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}|{text}'\n slot_uri: MIXS:0001070\n alias: tiss_cult_growth_med\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n toluene:\n name: toluene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of toluene in the sample\n title: toluene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - toluene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000154\n alias: toluene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_carb:\n name: tot_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total carbon content\n title: total carbon\n todos:\n - is this inorganic and organic? both? could use some clarification.\n - ug/L doesn't seem like the right units. Should check this slots usage in databases\n and re-evaluate. I couldn't find any references that provided this data in this\n format\n examples:\n - value: 1 ug/L\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000525\n alias: tot_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_depth_water_col:\n name: tot_depth_water_col\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of total depth of water column\n title: total depth of water column\n examples:\n - value: 500 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total depth of water column\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000634\n alias: tot_depth_water_col\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_diss_nitro:\n name: tot_diss_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\n title: total dissolved nitrogen\n examples:\n - value: 40 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total dissolved nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000744\n alias: tot_diss_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_inorg_nitro:\n name: tot_inorg_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total inorganic nitrogen content\n title: total inorganic nitrogen\n examples:\n - value: 40 microgram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total inorganic nitrogen\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000745\n alias: tot_inorg_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_iron:\n name: tot_iron\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, milligram per kilogram\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of total iron in the sample\n title: total iron\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total iron\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000105\n alias: tot_iron\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_nitro:\n name: tot_nitro\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total nitrogen concentration of water samples, calculated by: total\n nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n without filtering, reported as nitrogen'\n title: total nitrogen concentration\n examples:\n - value: 50 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total nitrogen concentration\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000102\n alias: tot_nitro\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_nitro_cont_meth:\n name: tot_nitro_cont_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the total nitrogen\n title: total nitrogen content method\n examples:\n - value: https://doi.org/10.2134/agronmonogr9.2.c32\n - value: https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/sssaj2009.0389?casa_token=bm0pYIUdNMgAAAAA%3AOWVRR0STHaOe-afTcTdxn5m1hM8n2ltM0wY-b1iYpYdD9dhwppk5j3LvC2IO5yhOIvyLVeQz4NZRCZo\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total nitrogen content method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000338\n alias: tot_nitro_cont_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n tot_nitro_content:\n name: tot_nitro_content\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total nitrogen content of the sample\n title: total nitrogen content\n examples:\n - value: 5 mg N/ L\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total nitrogen content\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000530\n alias: tot_nitro_content\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_org_c_meth:\n name: tot_org_c_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining total organic carbon\n title: total organic carbon method\n examples:\n - value: https://doi.org/10.1080/07352680902776556\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total organic carbon method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000337\n alias: tot_org_c_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n tot_org_carb:\n name: tot_org_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram Carbon per kilogram sample material\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Definition for soil: total organic carbon content of the soil, definition\n otherwise: total organic carbon content'\n title: total organic carbon\n todos:\n - check description. How are they different?\n examples:\n - value: 5 mg N/ L\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total organic carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000533\n alias: tot_org_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_part_carb:\n name: tot_part_carb\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total particulate carbon content\n title: total particulate carbon\n examples:\n - value: 35 micromole per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total particulate carbon\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000747\n alias: tot_part_carb\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_phosp:\n name: tot_phosp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: 'Total phosphorus concentration in the sample, calculated by: total\n phosphorus = total dissolved phosphorus + particulate phosphorus'\n title: total phosphorus\n examples:\n - value: 0.03 milligram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total phosphorus\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000117\n alias: tot_phosp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_phosphate:\n name: tot_phosphate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Total amount or concentration of phosphate\n title: total phosphate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total phosphate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000689\n alias: tot_phosphate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tot_sulfur:\n name: tot_sulfur\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of total sulfur in the sample\n title: total sulfur\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - total sulfur\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000419\n alias: tot_sulfur\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n train_line:\n name: train_line\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The subway line name\n title: train line\n examples:\n - value: red\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train line\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000837\n alias: train_line\n owner: Biosample\n domain_of:\n - Biosample\n range: train_line_enum\n multivalued: false\n train_stat_loc:\n name: train_stat_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The train station collection location\n title: train station collection location\n examples:\n - value: forest hills\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train station collection location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000838\n alias: train_stat_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: train_stat_loc_enum\n multivalued: false\n train_stop_loc:\n name: train_stop_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The train stop collection location\n title: train stop collection location\n examples:\n - value: end\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - train stop collection location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000839\n alias: train_stop_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: train_stop_loc_enum\n multivalued: false\n turbidity:\n name: turbidity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: formazin turbidity unit, formazin nephelometric units\n occurrence:\n tag: occurrence\n value: '1'\n description: Measure of the amount of cloudiness or haziness in water caused by\n individual particles\n title: turbidity\n examples:\n - value: 0.3 nephelometric turbidity units\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - turbidity\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000191\n alias: turbidity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tvdss_of_hcr_press:\n name: tvdss_of_hcr_press\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original pressure was measured (e.g. 1578 m).\n title: depth (TVDSS) of hydrocarbon resource pressure\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth (TVDSS) of hydrocarbon resource pressure\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000397\n alias: tvdss_of_hcr_press\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n tvdss_of_hcr_temp:\n name: tvdss_of_hcr_temp\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\n description: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original temperature was measured (e.g. 1345 m).\n title: depth (TVDSS) of hydrocarbon resource temperature\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - depth (TVDSS) of hydrocarbon resource temperature\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000394\n alias: tvdss_of_hcr_temp\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n typ_occup_density:\n name: typ_occup_density\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\n description: Customary or normal density of occupants\n title: typical occupant density\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - typical occupant density\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000771\n alias: typ_occup_density\n owner: Biosample\n domain_of:\n - Biosample\n range: double\n multivalued: false\n ventilation_rate:\n name: ventilation_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per minute, liters per second\n occurrence:\n tag: occurrence\n value: '1'\n description: Ventilation rate of the system in the sampled premises\n title: ventilation rate\n examples:\n - value: 750 cubic meter per minute\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ventilation rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000114\n alias: ventilation_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n ventilation_type:\n name: ventilation_type\n annotations:\n expected_value:\n tag: expected_value\n value: ventilation type name\n occurrence:\n tag: occurrence\n value: '1'\n description: Ventilation system used in the sampled premises\n title: ventilation type\n examples:\n - value: Operable windows\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - ventilation type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000756\n alias: ventilation_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n vfa:\n name: vfa\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of Volatile Fatty Acids in the sample\n title: volatile fatty acids\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volatile fatty acids\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000152\n alias: vfa\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n vfa_fw:\n name: vfa_fw\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\n description: Original volatile fatty acid concentration in the hydrocarbon resource\n title: vfa in formation water\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - vfa in formation water\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000408\n alias: vfa_fw\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n vis_media:\n name: vis_media\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building visual media\n title: visual media\n examples:\n - value: 3D scans\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - visual media\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000840\n alias: vis_media\n owner: Biosample\n domain_of:\n - Biosample\n range: vis_media_enum\n multivalued: false\n viscosity:\n name: viscosity\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: cP at degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\n title: viscosity\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - viscosity\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{float} {unit}'\n slot_uri: MIXS:0000126\n alias: viscosity\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n volatile_org_comp:\n name: volatile_org_comp\n annotations:\n expected_value:\n tag: expected_value\n value: volatile organic compound name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per cubic meter, parts per million, nanogram per liter\n occurrence:\n tag: occurrence\n value: m\n description: Concentration of carbon-based chemicals that easily evaporate at\n room temperature; can report multiple volatile organic compounds by entering\n numeric values preceded by name of compound\n title: volatile organic compounds\n examples:\n - value: formaldehyde;500 nanogram per liter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - volatile organic compounds\n rank: 1000\n is_a: core field\n string_serialization: '{text};{float} {unit}'\n slot_uri: MIXS:0000115\n alias: volatile_org_comp\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n wall_area:\n name: wall_area\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The total area of the sampled room's walls\n title: wall area\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall area\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000198\n alias: wall_area\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n wall_const_type:\n name: wall_const_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The building class of the wall defined by the composition of the\n building elements and fire-resistance rating.\n title: wall construction type\n examples:\n - value: fire resistive\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall construction type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000841\n alias: wall_const_type\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_const_type_enum\n multivalued: false\n wall_finish_mat:\n name: wall_finish_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The material utilized to finish the outer most layer of the wall\n title: wall finish material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall finish material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000842\n alias: wall_finish_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_finish_mat_enum\n multivalued: false\n wall_height:\n name: wall_height\n annotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\n description: The average height of the walls in the sampled room\n title: wall height\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall height\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000221\n alias: wall_height\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n wall_loc:\n name: wall_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the wall within the room\n title: wall location\n examples:\n - value: north\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000843\n alias: wall_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_loc_enum\n multivalued: false\n wall_surf_treatment:\n name: wall_surf_treatment\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The surface treatment of interior wall\n title: wall surface treatment\n examples:\n - value: paneling\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall surface treatment\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000845\n alias: wall_surf_treatment\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_surf_treatment_enum\n multivalued: false\n wall_texture:\n name: wall_texture\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The feel, appearance, or consistency of a wall surface\n title: wall texture\n examples:\n - value: popcorn\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall texture\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000846\n alias: wall_texture\n owner: Biosample\n domain_of:\n - Biosample\n range: wall_texture_enum\n multivalued: false\n wall_thermal_mass:\n name: wall_thermal_mass\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\n description: The ability of the wall to provide inertia against temperature fluctuations.\n Generally this means concrete or concrete block that is either exposed or covered\n only with paint\n title: wall thermal mass\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall thermal mass\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000222\n alias: wall_thermal_mass\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n wall_water_mold:\n name: wall_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on a wall\n title: wall signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wall signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000844\n alias: wall_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n wastewater_type:\n name: wastewater_type\n annotations:\n expected_value:\n tag: expected_value\n value: wastewater type name\n occurrence:\n tag: occurrence\n value: '1'\n description: The origin of wastewater such as human waste, rainfall, storm drains,\n etc.\n title: wastewater type\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wastewater type\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000353\n alias: wastewater_type\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n water_cont_soil_meth:\n name: water_cont_soil_meth\n annotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\n description: Reference or method used in determining the water content of soil\n title: water content method\n todos:\n - Why is it soil water content method in the name but not the title? Is this slot\n used in other samples?\n - Soil water content can be measure MANY ways and often, multiple ways are used\n in one experiment (gravimetric water content and water holding capacity and\n water filled pore space, to name a few).\n - Should this be multi valued? How to we manage and validate this?\n comments:\n - Required if providing water content\n examples:\n - value: J. Nat. Prod. Plant Resour., 2012, 2 (4):500-503\n - value: https://dec.alaska.gov/applications/spar/webcalc/definitions.htm\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water content method\n rank: 1000\n is_a: core field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000323\n alias: water_cont_soil_meth\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: false\n water_content:\n name: water_content\n annotations:\n expected_value:\n tag: expected_value\n value: string\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n description: Water content measurement\n title: water content\n todos:\n - value in preferred unit is too limiting. need to change this\n - check and correct validation so examples are accepted\n - how to manage multiple water content methods?\n examples:\n - value: 0.75 g water/g dry soil\n - value: 75% water holding capacity\n - value: 1.1 g fresh weight/ dry weight\n - value: 10% water filled pore space\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water content\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000185\n alias: water_content\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n water_current:\n name: water_current\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per second, knots\n occurrence:\n tag: occurrence\n value: '1'\n description: Measurement of magnitude and direction of flow within a fluid\n title: water current\n examples:\n - value: 10 cubic meter per second\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water current\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000203\n alias: water_current\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n water_cut:\n name: water_cut\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\n description: Current amount of water (%) in a produced fluid stream; or the average\n of the combined streams\n title: water cut\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water cut\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000454\n alias: water_cut\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n water_feat_size:\n name: water_feat_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The size of the water feature\n title: water feature size\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water feature size\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000223\n alias: water_feat_size\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n water_feat_type:\n name: water_feat_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of water feature present within the building being sampled\n title: water feature type\n examples:\n - value: stream\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water feature type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000847\n alias: water_feat_type\n owner: Biosample\n domain_of:\n - Biosample\n range: water_feat_type_enum\n multivalued: false\n water_prod_rate:\n name: water_prod_rate\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\n description: Water production rates per well (e.g. 987 m3 / day)\n title: water production rate\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water production rate\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000453\n alias: water_prod_rate\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n water_temp_regm:\n name: water_temp_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to water with varying\n degree of temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of\n the entire treatment; can include multiple regimens\n title: water temperature regimen\n examples:\n - value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - water temperature regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000590\n alias: water_temp_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n watering_regm:\n name: watering_regm\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milliliter, liter\n occurrence:\n tag: occurrence\n value: m\n description: Information about treatment involving an exposure to watering frequencies,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can\n include multiple regimens\n title: watering regimen\n examples:\n - value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\n - value: 75% water holding capacity; constant\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - watering regimen\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\n slot_uri: MIXS:0000591\n alias: watering_regm\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n weekday:\n name: weekday\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The day of the week when sampling occurred\n title: weekday\n examples:\n - value: Sunday\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - weekday\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000848\n alias: weekday\n owner: Biosample\n domain_of:\n - Biosample\n range: weekday_enum\n multivalued: false\n win:\n name: win\n annotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\n description: 'A unique identifier of a well or wellbore. This is part of the Global\n Framework for Well Identification initiative which is compiled by the Professional\n Petroleum Data Management Association (PPDM) in an effort to improve well identification\n systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\n title: well identification number\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - well identification number\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000297\n alias: win\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n wind_direction:\n name: wind_direction\n annotations:\n expected_value:\n tag: expected_value\n value: wind direction name\n occurrence:\n tag: occurrence\n value: '1'\n description: Wind direction is the direction from which a wind originates\n title: wind direction\n examples:\n - value: Northwest\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wind direction\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000757\n alias: wind_direction\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n wind_speed:\n name: wind_speed\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second, kilometer per hour\n occurrence:\n tag: occurrence\n value: '1'\n description: Speed of wind measured at the time of sampling\n title: wind speed\n examples:\n - value: 21 kilometer per hour\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - wind speed\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000118\n alias: wind_speed\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n window_cond:\n name: window_cond\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The physical condition of the window at the time of sampling\n title: window condition\n examples:\n - value: rupture\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window condition\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000849\n alias: window_cond\n owner: Biosample\n domain_of:\n - Biosample\n range: window_cond_enum\n multivalued: false\n window_cover:\n name: window_cover\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of window covering\n title: window covering\n examples:\n - value: curtains\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window covering\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000850\n alias: window_cover\n owner: Biosample\n domain_of:\n - Biosample\n range: window_cover_enum\n multivalued: false\n window_horiz_pos:\n name: window_horiz_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The horizontal position of the window on the wall\n title: window horizontal position\n examples:\n - value: middle\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window horizontal position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000851\n alias: window_horiz_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: window_horiz_pos_enum\n multivalued: false\n window_loc:\n name: window_loc\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The relative location of the window within the room\n title: window location\n examples:\n - value: west\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window location\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000852\n alias: window_loc\n owner: Biosample\n domain_of:\n - Biosample\n range: window_loc_enum\n multivalued: false\n window_mat:\n name: window_mat\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of material used to finish a window\n title: window material\n examples:\n - value: wood\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window material\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000853\n alias: window_mat\n owner: Biosample\n domain_of:\n - Biosample\n range: window_mat_enum\n multivalued: false\n window_open_freq:\n name: window_open_freq\n annotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\n description: The number of times windows are opened per week\n title: window open frequency\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window open frequency\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000246\n alias: window_open_freq\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n window_size:\n name: window_size\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: inch, meter\n occurrence:\n tag: occurrence\n value: '1'\n description: The window's length and width\n title: window area/size\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window area/size\n rank: 1000\n is_a: core field\n string_serialization: '{float} {unit} x {float} {unit}'\n slot_uri: MIXS:0000224\n alias: window_size\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n window_status:\n name: window_status\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Defines whether the windows were open or closed during environmental\n testing\n title: window status\n examples:\n - value: open\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window status\n rank: 1000\n is_a: core field\n string_serialization: '[closed|open]'\n slot_uri: MIXS:0000855\n alias: window_status\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n window_type:\n name: window_type\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The type of windows\n title: window type\n examples:\n - value: fixed window\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window type\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000856\n alias: window_type\n owner: Biosample\n domain_of:\n - Biosample\n range: window_type_enum\n multivalued: false\n window_vert_pos:\n name: window_vert_pos\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: The vertical position of the window on the wall\n title: window vertical position\n examples:\n - value: middle\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window vertical position\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000857\n alias: window_vert_pos\n owner: Biosample\n domain_of:\n - Biosample\n range: window_vert_pos_enum\n multivalued: false\n window_water_mold:\n name: window_water_mold\n annotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\n description: Signs of the presence of mold or mildew on the window.\n title: window signs of water/mold\n examples:\n - value: no presence of mold visible\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - window signs of water/mold\n rank: 1000\n is_a: core field\n string_serialization: '[presence of mold visible|no presence of mold visible]'\n slot_uri: MIXS:0000854\n alias: window_water_mold\n owner: Biosample\n domain_of:\n - Biosample\n range: TextValue\n multivalued: false\n xylene:\n name: xylene\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of xylene in the sample\n title: xylene\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - xylene\n rank: 1000\n is_a: core field\n slot_uri: MIXS:0000156\n alias: xylene\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n multivalued: false\n zinc:\n name: zinc\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\n description: Concentration of zinc in the sample\n title: zinc\n examples:\n - value: 2.5 mg/kg\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ornl.gov/content/bio-scales-0\n aliases:\n - zinc\n rank: 1000\n alias: zinc\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: Biosample\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n community:\n name: community\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: community\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n habitat:\n name: habitat\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: habitat\n owner: Biosample\n domain_of:\n - FieldResearchSite\n - Biosample\n range: string\n host_name:\n name: host_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: host_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n location:\n name: location\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: location\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: Biosample\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n ncbi_taxonomy_name:\n name: ncbi_taxonomy_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_taxonomy_name\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n proport_woa_temperature:\n name: proport_woa_temperature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: proport_woa_temperature\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n salinity_category:\n name: salinity_category\n description: 'Categorical description of the sample''s salinity. Examples: halophile,\n halotolerant, hypersaline, huryhaline'\n notes:\n - maps to gold:salinity\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-metadata/pull/297\n rank: 1000\n alias: salinity_category\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n sample_collection_site:\n name: sample_collection_site\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sample_collection_site\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n soluble_iron_micromol:\n name: soluble_iron_micromol\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: soluble_iron_micromol\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n subsurface_depth:\n name: subsurface_depth\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: subsurface_depth\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n dna_absorb1:\n name: dna_absorb1\n description: 260/280 measurement of DNA sample purity\n title: DNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n alias: dna_absorb1\n owner: Biosample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_absorb2:\n name: dna_absorb2\n description: 260/230 measurement of DNA sample purity\n title: DNA absorbance 260/230\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n is_a: biomaterial_purity\n alias: dna_absorb2\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_collect_site:\n name: dna_collect_site\n description: Provide information on the site your DNA sample was collected from\n title: DNA collection site\n examples:\n - value: untreated pond water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: dna_collect_site\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_concentration:\n name: dna_concentration\n title: DNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n alias: dna_concentration\n owner: Biosample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n dna_cont_type:\n name: dna_cont_type\n description: Tube or plate (96-well)\n title: DNA container type\n examples:\n - value: plate\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n alias: dna_cont_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: JgiContTypeEnum\n recommended: true\n dna_container_id:\n name: dna_container_id\n title: DNA container label\n comments:\n - Must be unique across all tubes and plates, and <20 characters. All samples\n in a plate should have the same plate label.\n examples:\n - value: Pond_MT_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{text < 20 characters}'\n alias: dna_container_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_dnase:\n name: dna_dnase\n title: DNase treatment DNA\n comments:\n - Note DNase treatment is required for all RNA samples.\n examples:\n - value: 'no'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 13\n alias: dna_dnase\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: YesNoEnum\n recommended: true\n dna_isolate_meth:\n name: dna_isolate_meth\n description: Describe the method/protocol/kit used to extract DNA/RNA.\n title: DNA isolation method\n examples:\n - value: phenol/chloroform extraction\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Sample Isolation Method\n rank: 16\n string_serialization: '{text}'\n alias: dna_isolate_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_organisms:\n name: dna_organisms\n description: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\n title: DNA expected organisms\n examples:\n - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n (1%)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{text}'\n alias: dna_organisms\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_project_contact:\n name: dna_project_contact\n title: DNA seq project contact\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: John Jones\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 18\n string_serialization: '{text}'\n alias: dna_project_contact\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_samp_id:\n name: dna_samp_id\n title: DNA sample ID\n todos:\n - Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n have two identifiers. How to force uniqueness? Moot because that column will\n be prefilled?\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '187654'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{text}'\n alias: dna_samp_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_sample_format:\n name: dna_sample_format\n description: Solution in which the DNA sample has been suspended\n title: DNA sample format\n examples:\n - value: Water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n alias: dna_sample_format\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: DNASampleFormatEnum\n recommended: true\n dna_sample_name:\n name: dna_sample_name\n description: Give the DNA sample a name that is meaningful to you. Sample names\n must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n title: DNA sample name\n examples:\n - value: JGI_pond_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{text}'\n alias: dna_sample_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project:\n name: dna_seq_project\n title: DNA seq project ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '1191234'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Seq Project ID\n rank: 1\n string_serialization: '{text}'\n alias: dna_seq_project\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project_pi:\n name: dna_seq_project_pi\n title: DNA seq project PI\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: Jane Johnson\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 17\n string_serialization: '{text}'\n alias: dna_seq_project_pi\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_seq_project_name:\n name: dna_seq_project_name\n title: DNA seq project name\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: JGI Pond metagenomics\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{text}'\n alias: dna_seq_project_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dna_volume:\n name: dna_volume\n title: DNA volume in ul\n comments:\n - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n form accepts values < 25, but JGI may refuse to process them unless permission\n has been granted by a project manager\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{float}'\n alias: dna_volume\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n proposal_dna:\n name: proposal_dna\n title: DNA proposal ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '504000'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 19\n string_serialization: '{text}'\n alias: proposal_dna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metagenomics\n range: string\n recommended: true\n dnase_rna:\n name: dnase_rna\n title: DNase treated\n comments:\n - Note DNase treatment is required for all RNA samples.\n examples:\n - value: 'no'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Was Sample DNAse treated?\n rank: 13\n alias: dnase_rna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: YesNoEnum\n recommended: true\n proposal_rna:\n name: proposal_rna\n title: RNA proposal ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '504000'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 19\n string_serialization: '{text}'\n alias: proposal_rna\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_absorb1:\n name: rna_absorb1\n description: 260/280 measurement of RNA sample purity\n title: RNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n string_serialization: '{float}'\n alias: rna_absorb1\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n rna_absorb2:\n name: rna_absorb2\n description: 260/230 measurement of RNA sample purity\n title: RNA absorbance 260/230\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 8\n string_serialization: '{float}'\n alias: rna_absorb2\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n rna_collect_site:\n name: rna_collect_site\n description: Provide information on the site your RNA sample was collected from\n title: RNA collection site\n examples:\n - value: untreated pond water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 15\n string_serialization: '{text}'\n alias: rna_collect_site\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_concentration:\n name: rna_concentration\n title: RNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n string_serialization: '{float}'\n alias: rna_concentration\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n rna_cont_type:\n name: rna_cont_type\n description: Tube or plate (96-well)\n title: RNA container type\n examples:\n - value: plate\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 10\n alias: rna_cont_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: JgiContTypeEnum\n recommended: true\n rna_cont_well:\n name: rna_cont_well\n title: RNA plate position\n comments:\n - Required when 'plate' is selected for container type.\n - Leave blank if the sample will be shipped in a tube.\n - JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not\n pass validation.\n - For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\n examples:\n - value: B2\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 11\n string_serialization: '{96 well plate pos}'\n alias: rna_cont_well\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n rna_container_id:\n name: rna_container_id\n title: RNA container label\n comments:\n - Must be unique across all tubes and plates, and <20 characters. All samples\n in a plate should have the same plate label.\n examples:\n - value: Pond_MT_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 9\n string_serialization: '{text < 20 characters}'\n alias: rna_container_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_isolate_meth:\n name: rna_isolate_meth\n description: Describe the method/protocol/kit used to extract DNA/RNA.\n title: RNA isolation method\n examples:\n - value: phenol/chloroform extraction\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Sample Isolation Method\n rank: 16\n string_serialization: '{text}'\n alias: rna_isolate_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_organisms:\n name: rna_organisms\n description: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\n title: RNA expected organisms\n examples:\n - value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles\n (1%)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 14\n string_serialization: '{text}'\n alias: rna_organisms\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_project_contact:\n name: rna_project_contact\n title: RNA seq project contact\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: John Jones\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 18\n string_serialization: '{text}'\n alias: rna_project_contact\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_samp_id:\n name: rna_samp_id\n title: RNA sample ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '187654'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{text}'\n alias: rna_samp_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_sample_format:\n name: rna_sample_format\n description: Solution in which the RNA sample has been suspended\n title: RNA sample format\n examples:\n - value: Water\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 12\n alias: rna_sample_format\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: RNASampleFormatEnum\n recommended: true\n rna_sample_name:\n name: rna_sample_name\n description: Give the RNA sample a name that is meaningful to you. Sample names\n must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\n title: RNA sample name\n examples:\n - value: JGI_pond_041618\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 4\n string_serialization: '{text}'\n alias: rna_sample_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n rna_seq_project:\n name: rna_seq_project\n title: RNA seq project ID\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: '1191234'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Seq Project ID\n rank: 1\n string_serialization: '{text}'\n alias: rna_seq_project\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_seq_project_pi:\n name: rna_seq_project_pi\n title: RNA seq project PI\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: Jane Johnson\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 17\n string_serialization: '{text}'\n alias: rna_seq_project_pi\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_seq_project_name:\n name: rna_seq_project_name\n title: RNA seq project name\n comments:\n - Do not edit these values. A template will be provided by NMDC in which these\n values have been pre-filled.\n examples:\n - value: JGI Pond metatranscriptomics\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n string_serialization: '{text}'\n alias: rna_seq_project_name\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: string\n recommended: true\n rna_volume:\n name: rna_volume\n title: RNA volume in ul\n comments:\n - Units must be in uL. Enter the numerical part only. Value must be 0-1000. This\n form accepts values < 25, but JGI may refuse to process them unless permission\n has been granted by a project manager\n examples:\n - value: '25'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{float}'\n alias: rna_volume\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: JGI-Metatranscriptomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 1000\n collection_date_inc:\n name: collection_date_inc\n description: Date the incubation was harvested/collected/ended. Only relevant\n for incubation samples.\n title: incubation collection date\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\n comments:\n - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n are all acceptable.\n examples:\n - value: '2021-04-15'\n - value: 2021-04\n - value: '2021'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 2\n string_serialization: '{date, arbitrary precision}'\n alias: collection_date_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n collection_time:\n name: collection_time\n description: The time of sampling, either as an instance (single point) or interval.\n title: collection time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: '13:33'\n - value: '13:33:55'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 1\n string_serialization: '{time, seconds optional}'\n alias: collection_time\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n collection_time_inc:\n name: collection_time_inc\n description: Time the incubation was harvested/collected/ended. Only relevant\n for incubation samples.\n title: incubation collection time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: '13:33'\n - value: '13:33:55'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 3\n string_serialization: '{time, seconds optional}'\n alias: collection_time_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n experimental_factor_other:\n name: experimental_factor_other\n description: Other details about your sample that you feel can't be accurately\n represented in the available columns.\n title: experimental factor- other\n comments:\n - This slot accepts open-ended text about your sample.\n - We recommend using key:value pairs.\n - Provided pairs will be considered for inclusion as future slots/terms in this\n data collection template.\n examples:\n - value: 'experimental treatment: value'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000008\n - MIXS:0000300\n rank: 7\n string_serialization: '{text}'\n alias: experimental_factor_other\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n filter_method:\n name: filter_method\n description: Type of filter used or how the sample was filtered\n title: filter method\n comments:\n - describe the filter or provide a catalog number and manufacturer\n examples:\n - value: C18\n - value: Basix PES, 13-100-106 FisherSci\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000765\n rank: 6\n string_serialization: '{text}'\n alias: filter_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n isotope_exposure:\n name: isotope_exposure\n description: List isotope exposure or addition applied to your sample.\n title: isotope exposure/addition\n todos:\n - Can we make the H218O correctly super and subscripted?\n comments:\n - This is required when your experimental design includes the use of isotopically\n labeled compounds\n examples:\n - value: 13C glucose\n - value: 18O water\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000751\n rank: 16\n alias: isotope_exposure\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n micro_biomass_c_meth:\n name: micro_biomass_c_meth\n description: Reference or method used in determining microbial biomass carbon\n title: microbial biomass carbon method\n todos:\n - How should we separate values? | or ;? lets be consistent\n comments:\n - required if \"microbial_biomass_c\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(87)90052-6\n - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000339\n rank: 11\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: micro_biomass_c_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n micro_biomass_n_meth:\n name: micro_biomass_n_meth\n description: Reference or method used in determining microbial biomass nitrogen\n title: microbial biomass nitrogen method\n comments:\n - required if \"microbial_biomass_n\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(87)90052-6\n - value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000339\n rank: 13\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: micro_biomass_n_meth\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n microbial_biomass_c:\n name: microbial_biomass_c\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer.\n title: microbial biomass carbon\n comments:\n - If you provide this, correction factors used for conversion to the final units\n and method are required\n examples:\n - value: 0.05 ug C/g dry soil\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000650\n rank: 10\n string_serialization: '{float} {unit}'\n alias: microbial_biomass_c\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n microbial_biomass_n:\n name: microbial_biomass_n\n description: The part of the organic matter in the soil that constitutes living\n microorganisms smaller than 5-10 micrometer.\n title: microbial biomass nitrogen\n comments:\n - If you provide this, correction factors used for conversion to the final units\n and method are required\n examples:\n - value: 0.05 ug N/g dry soil\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000650\n rank: 12\n string_serialization: '{float} {unit}'\n alias: microbial_biomass_n\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n non_microb_biomass:\n name: non_microb_biomass\n description: Amount of biomass; should include the name for the part of biomass\n measured, e.g.insect, plant, total. Can include multiple measurements separated\n by ;\n title: non-microbial biomass\n examples:\n - value: insect 0.23 ug; plant 1g\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000174\n - MIXS:0000650\n rank: 8\n string_serialization: '{text};{float} {unit}'\n alias: non_microb_biomass\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n non_microb_biomass_method:\n name: non_microb_biomass_method\n description: Reference or method used in determining biomass\n title: non-microbial biomass method\n comments:\n - required if \"non-microbial biomass\" is provided\n examples:\n - value: https://doi.org/10.1038/s41467-021-26181-3\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000650\n rank: 9\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: non_microb_biomass_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n org_nitro_method:\n name: org_nitro_method\n description: Method used for obtaining organic nitrogen\n title: organic nitrogen method\n comments:\n - required if \"org_nitro\" is provided\n examples:\n - value: https://doi.org/10.1016/0038-0717(85)90144-0\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000338\n - MIXS:0000205\n rank: 14\n string_serialization: '{PMID}|{DOI}|{URL}'\n alias: org_nitro_method\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n other_treatment:\n name: other_treatment\n description: Other treatments applied to your samples that are not applicable\n to the provided fields\n title: other treatments\n notes:\n - Values entered here will be used to determine potential new slots.\n comments:\n - This is an open text field to provide any treatments that cannot be captured\n in the provided slots.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000300\n rank: 15\n string_serialization: '{text}'\n alias: other_treatment\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n start_date_inc:\n name: start_date_inc\n description: Date the incubation was started. Only relevant for incubation samples.\n title: incubation start date\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\n comments:\n - Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021\n are all acceptable.\n examples:\n - value: '2021-04-15'\n - value: 2021-04\n - value: '2021'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 4\n string_serialization: '{date, arbitrary precision}'\n alias: start_date_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n start_time_inc:\n name: start_time_inc\n description: Time the incubation was started. Only relevant for incubation samples.\n title: incubation start time, GMT\n notes:\n - MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional\n time only\n comments:\n - 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\n examples:\n - value: '13:33'\n - value: '13:33:55'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIXS:0000011\n rank: 5\n string_serialization: '{time, seconds optional}'\n alias: start_time_inc\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: MIxS Inspired\n range: string\n recommended: true\n project_id:\n name: project_id\n description: Proposal IDs or names associated with dataset\n title: project ID\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1\n string_serialization: '{text}'\n alias: project_id\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n replicate_number:\n name: replicate_number\n description: If sending biological replicates, indicate the rep number here.\n title: replicate number\n comments:\n - This will guide staff in ensuring your samples are blocked & randomized correctly\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 6\n string_serialization: '{integer}'\n alias: replicate_number\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n sample_shipped:\n name: sample_shipped\n description: The total amount or size (volume (ml), mass (g) or area (m2) ) of\n sample sent to EMSL.\n title: sample shipped amount\n comments:\n - This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\n examples:\n - value: 15 g\n - value: 100 uL\n - value: 5 mL\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 3\n string_serialization: '{float} {unit}'\n alias: sample_shipped\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n sample_type:\n name: sample_type\n description: Type of sample being submitted\n title: sample type\n comments:\n - This can vary from 'environmental package' if the sample is an extraction.\n examples:\n - value: water extracted soil\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 2\n alias: sample_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: SampleTypeEnum\n recommended: true\n technical_reps:\n name: technical_reps\n description: If sending technical replicates of the same sample, indicate the\n replicate count.\n title: number technical replicate\n comments:\n - This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\n examples:\n - value: '2'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{integer}'\n alias: technical_reps\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: EMSL\n range: string\n recommended: true\n analysis_type:\n name: analysis_type\n description: Select all the data types associated or available for this biosample\n title: analysis/data type\n examples:\n - value: metagenomics; metabolomics; metaproteomics\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - MIxS:investigation_type\n rank: 3\n alias: analysis_type\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: Sample ID\n range: AnalysisTypeEnum\n recommended: true\n multivalued: true\n sample_link:\n name: sample_link\n description: A unique identifier to assign parent-child, subsample, or sibling\n samples. This is relevant when a sample or other material was used to generate\n the new sample.\n title: sample linkage\n comments:\n - 'This field allows multiple entries separated by ; (Examples: Soil collected\n from the field will link with the soil used in an incubation. The soil a plant\n was grown in links to the plant sample. An original culture sample was transferred\n to a new vial and generated a new sample)'\n examples:\n - value: IGSN:DSJ0284\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 5\n string_serialization: '{text}:{text}'\n alias: sample_link\n owner: Biosample\n domain_of:\n - Biosample\n slot_group: Sample ID\n range: string\n recommended: true\n multivalued: true\n bulk_elect_conductivity:\n name: bulk_elect_conductivity\n description: Electrical conductivity is a measure of the ability to carry electric\n current, which is mostly dictated by the chemistry of and amount of water.\n title: bulk electrical conductivity\n comments:\n - Provide the value output of the field instrument.\n examples:\n - value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')\n description: The conductivity measurement was 0.017 millisiemens per centimeter.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bulk_elect_conductivity\n owner: Biosample\n domain_of:\n - Biosample\n range: QuantityValue\n infiltrations:\n name: infiltrations\n description: The amount of time it takes to complete each infiltration activity\n examples:\n - value: '[''00:01:32'', ''00:00:53'']'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1\n aliases:\n - infiltration_1\n - infiltration_2\n rank: 1000\n list_elements_ordered: true\n alias: infiltrations\n owner: Biosample\n domain_of:\n - Biosample\n range: string\n multivalued: true\n pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$\n id:\n name: id\n description: An NMDC assigned unique identifier for a biosample submitted to NMDC.\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Biosample\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Biosample\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Biosample\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A uriorcurie reference to an external database or resource that provides\n additional information or context about a specific entity at NMDC.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Biosample\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Biosample\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Biosample\nunique_keys:\n samp_name_unique_key:\n unique_key_name: samp_name_unique_key\n unique_key_slots:\n - samp_name\nrules:\n- preconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n description: DNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: dna_well_requires_plate\n- preconditions:\n slot_conditions:\n dna_cont_type:\n name: dna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n dna_cont_well:\n name: dna_cont_well\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n description: DNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: dna_plate_requires_well\n- preconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: .+\n postconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n description: RNA samples shipped to JGI for metagenomic analysis in tubes can't\n have any value for their plate position.\n title: rna_well_requires_plate\n- preconditions:\n slot_conditions:\n rna_cont_type:\n name: rna_cont_type\n equals_string: plate\n postconditions:\n slot_conditions:\n rna_cont_well:\n name: rna_cont_well\n pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n description: RNA samples in plates must have a plate position that matches the regex.\n Note the requirement for an empty string in the tube case. Waiting for value_present\n validation to be added to runtime\n title: rna_plate_requires_well\n\nFunding-based, sample location-based, or experimental method-based defined categories
URI: BiosampleCategoryEnum
"},{"location":"BiosampleCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description LTER https://lternet.edu/ SIP None SFA https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance Science Focus Area projects funded through the Department of Energy Office of... FICUS https://jgi.doe.gov/user-programs/program-info/ficus-overview NEON https://www.neonscience.org"},{"location":"BiosampleCategoryEnum/#slots","title":"Slots","text":"Name Description biosample_categories"},{"location":"BiosampleCategoryEnum/#aliases","title":"Aliases","text":"name: BiosampleCategoryEnum\ndescription: Funding-based, sample location-based, or experimental method-based defined\n categories\nnotes:\n- Currently, these values can associated with biosamples via the biosample_categories\n slot\n- They might also be applicable to other classes\n- They are intended to enable metadata search and or filtering, for example in the\n NMDC data portal, https://data.microbiomedata.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- category tag\nrank: 1000\npermissible_values:\n LTER:\n text: LTER\n meaning: https://lternet.edu/\n title: National Science Foundation's Long Term Ecological Research Network\n SIP:\n text: SIP\n SFA:\n text: SFA\n description: Science Focus Area projects funded through the Department of Energy\n Office of Science Biological and Environmental Research Program\n meaning: https://science.osti.gov/ber/funding-opportunities/laboratory-scientific-focus-area-guidance\n title: Department of Energy Office of Science Biological and Environmental Research\n Program Laboratory Science Focus Areas\n FICUS:\n text: FICUS\n meaning: https://jgi.doe.gov/user-programs/program-info/ficus-overview\n title: Facilities Integrating Collaborations for User Science\n NEON:\n text: NEON\n meaning: https://www.neonscience.org\n title: National Science Foundation's National Ecological Observatory Network\n\nURI: BioticRelationshipEnum
"},{"location":"BioticRelationshipEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description free living None parasite None commensal None symbiont None"},{"location":"BioticRelationshipEnum/#slots","title":"Slots","text":"Name Description biotic_relationship Description of relationship(s) between the subject organism and other organis..."},{"location":"BioticRelationshipEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BioticRelationshipEnum/#schema-source","title":"Schema Source","text":"name: biotic_relationship_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n free living:\n text: free living\n parasite:\n text: parasite\n commensal:\n text: commensal\n symbiont:\n text: symbiont\n\nA binary (true or false) value
URI: xsd:boolean
base: Bool
uri: xsd:boolean
repr: bool
URI: BuildDocsEnum
"},{"location":"BuildDocsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description building information model None commissioning report None complaint logs None contract administration None cost estimate None janitorial schedules or logs None maintenance plans None schedule None sections None shop drawings None submittals None ventilation system None windows None"},{"location":"BuildDocsEnum/#slots","title":"Slots","text":"Name Description build_docs The building design, construction and operation documents"},{"location":"BuildDocsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildDocsEnum/#schema-source","title":"Schema Source","text":"name: build_docs_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n building information model:\n text: building information model\n commissioning report:\n text: commissioning report\n complaint logs:\n text: complaint logs\n contract administration:\n text: contract administration\n cost estimate:\n text: cost estimate\n janitorial schedules or logs:\n text: janitorial schedules or logs\n maintenance plans:\n text: maintenance plans\n schedule:\n text: schedule\n sections:\n text: sections\n shop drawings:\n text: shop drawings\n submittals:\n text: submittals\n ventilation system:\n text: ventilation system\n windows:\n text: windows\n\nURI: BuildOccupTypeEnum
"},{"location":"BuildOccupTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description office None market None restaurant None residence None school None residential None commercial None low rise None high rise None wood framed None health care None airport None sports complex None"},{"location":"BuildOccupTypeEnum/#slots","title":"Slots","text":"Name Description build_occup_type The primary function for which a building or discrete part of a building is i..."},{"location":"BuildOccupTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildOccupTypeEnum/#schema-source","title":"Schema Source","text":"name: build_occup_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n office:\n text: office\n market:\n text: market\n restaurant:\n text: restaurant\n residence:\n text: residence\n school:\n text: school\n residential:\n text: residential\n commercial:\n text: commercial\n low rise:\n text: low rise\n high rise:\n text: high rise\n wood framed:\n text: wood framed\n health care:\n text: health care\n airport:\n text: airport\n sports complex:\n text: sports complex\n\nURI: BuildingSettingEnum
"},{"location":"BuildingSettingEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description urban None suburban None exurban None rural None"},{"location":"BuildingSettingEnum/#slots","title":"Slots","text":"Name Description building_setting A location (geography) where a building is set"},{"location":"BuildingSettingEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"BuildingSettingEnum/#schema-source","title":"Schema Source","text":"name: building_setting_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n urban:\n text: urban\n suburban:\n text: suburban\n exurban:\n text: exurban\n rural:\n text: rural\n\nAn integer value that corresponds to a size in bytes
URI: xsd:long
base: int
uri: xsd:long
A calibration object that is associated with a process.
URI: nmdc:CalibrationInformation
classDiagram\n class CalibrationInformation\n click CalibrationInformation href \"../CalibrationInformation\"\n InformationObject <|-- CalibrationInformation\n click InformationObject href \"../InformationObject\"\n\n\n\n CalibrationInformation : alternative_identifiers\n\n CalibrationInformation : calibration_object\n\n CalibrationInformation --> \"0..1\" DataObject : calibration_object\n click DataObject href \"../DataObject\"\n\n CalibrationInformation : calibration_standard\n\n CalibrationInformation --> \"0..1\" CalibrationStandardEnum : calibration_standard\n click CalibrationStandardEnum href \"../CalibrationStandardEnum\"\n\n CalibrationInformation : calibration_target\n\n CalibrationInformation --> \"1\" CalibrationTargetEnum : calibration_target\n click CalibrationTargetEnum href \"../CalibrationTargetEnum\"\n\n CalibrationInformation : description\n\n CalibrationInformation : id\n\n CalibrationInformation : internal_calibration\n\n CalibrationInformation : name\n\n CalibrationInformation : type\n\n\n\nname: CalibrationInformation\ndescription: A calibration object that is associated with a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- calibration_object\n- internal_calibration\n- calibration_target\n- calibration_standard\nslot_usage:\n internal_calibration:\n name: internal_calibration\n required: true\n calibration_target:\n name: calibration_target\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:CalibrationInformation\nrules:\n- preconditions:\n slot_conditions:\n calibration_target:\n name: calibration_target\n equals_string: retention_index\n postconditions:\n slot_conditions:\n calibration_standard:\n name: calibration_standard\n required: true\n description: If the calibration_target is retention_index, a calibration_standard\n is required.\n title: calibration_standard_if_rt\n- preconditions:\n slot_conditions:\n internal_calibration:\n name: internal_calibration\n id_prefixes:\n - 'False'\n postconditions:\n slot_conditions:\n calibration_object:\n name: calibration_object\n required: true\n description: If internal_calibration is false, a calibration_object is required.\n title: calibration_object_if_not_internal_calibration\n\nname: CalibrationInformation\ndescription: A calibration object that is associated with a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n internal_calibration:\n name: internal_calibration\n required: true\n calibration_target:\n name: calibration_target\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n calibration_object:\n name: calibration_object\n description: the file containing calibration data object\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: calibration_object\n owner: CalibrationInformation\n domain_of:\n - CalibrationInformation\n range: DataObject\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n internal_calibration:\n name: internal_calibration\n description: whether internal calibration was used, if false, external calibration\n was used\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: internal_calibration\n owner: CalibrationInformation\n domain_of:\n - CalibrationInformation\n range: boolean\n required: true\n calibration_target:\n name: calibration_target\n description: the target measurement of the calibration\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: calibration_target\n owner: CalibrationInformation\n domain_of:\n - CalibrationInformation\n range: CalibrationTargetEnum\n required: true\n calibration_standard:\n name: calibration_standard\n description: the reference standard(s) used for calibration\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: calibration_standard\n owner: CalibrationInformation\n domain_of:\n - CalibrationInformation\n range: CalibrationStandardEnum\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: CalibrationInformation\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: CalibrationInformation\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: CalibrationInformation\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: CalibrationInformation\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: CalibrationInformation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:CalibrationInformation\nrules:\n- preconditions:\n slot_conditions:\n calibration_target:\n name: calibration_target\n equals_string: retention_index\n postconditions:\n slot_conditions:\n calibration_standard:\n name: calibration_standard\n required: true\n description: If the calibration_target is retention_index, a calibration_standard\n is required.\n title: calibration_standard_if_rt\n- preconditions:\n slot_conditions:\n internal_calibration:\n name: internal_calibration\n id_prefixes:\n - 'False'\n postconditions:\n slot_conditions:\n calibration_object:\n name: calibration_object\n required: true\n description: If internal_calibration is false, a calibration_object is required.\n title: calibration_object_if_not_internal_calibration\n\nURI: CalibrationStandardEnum
"},{"location":"CalibrationStandardEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fames None alkanes None"},{"location":"CalibrationStandardEnum/#slots","title":"Slots","text":"Name Description calibration_standard the reference standard(s) used for calibration"},{"location":"CalibrationStandardEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationStandardEnum/#schema-source","title":"Schema Source","text":"name: CalibrationStandardEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n fames:\n text: fames\n aliases:\n - FAMES\n alkanes:\n text: alkanes\n aliases:\n - Alkanes\n\nURI: CalibrationTargetEnum
"},{"location":"CalibrationTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mass_charge_ratio None retention_time None retention_index None"},{"location":"CalibrationTargetEnum/#slots","title":"Slots","text":"Name Description calibration_target the target measurement of the calibration"},{"location":"CalibrationTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CalibrationTargetEnum/#schema-source","title":"Schema Source","text":"name: CalibrationTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n mass_charge_ratio:\n text: mass_charge_ratio\n title: m/z\n aliases:\n - Mass\n - m/z\n retention_time:\n text: retention_time\n aliases:\n - RT\n retention_index:\n text: retention_index\n aliases:\n - RI\n\nURI: CeilCondEnum
"},{"location":"CeilCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"CeilCondEnum/#slots","title":"Slots","text":"Name Description ceil_cond The physical condition of the ceiling at the time of sampling; photos or vide..."},{"location":"CeilCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilCondEnum/#schema-source","title":"Schema Source","text":"name: ceil_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nURI: CeilFinishMatEnum
"},{"location":"CeilFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drywall None mineral fibre None tiles None PVC None plasterboard None metal None fiberglass None stucco None mineral wool/calcium silicate None wood None"},{"location":"CeilFinishMatEnum/#slots","title":"Slots","text":"Name Description ceil_finish_mat The type of material used to finish a ceiling"},{"location":"CeilFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilFinishMatEnum/#schema-source","title":"Schema Source","text":"name: ceil_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n drywall:\n text: drywall\n mineral fibre:\n text: mineral fibre\n tiles:\n text: tiles\n PVC:\n text: PVC\n plasterboard:\n text: plasterboard\n metal:\n text: metal\n fiberglass:\n text: fiberglass\n stucco:\n text: stucco\n mineral wool/calcium silicate:\n text: mineral wool/calcium silicate\n wood:\n text: wood\n\nURI: CeilTextureEnum
"},{"location":"CeilTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"CeilTextureEnum/#slots","title":"Slots","text":"Name Description ceil_texture The feel, appearance, or consistency of a ceiling surface"},{"location":"CeilTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTextureEnum/#schema-source","title":"Schema Source","text":"name: ceil_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crows feet:\n text: crows feet\n crows-foot stomp:\n text: crows-foot stomp\n double skip:\n text: double skip\n hawk and trowel:\n text: hawk and trowel\n knockdown:\n text: knockdown\n popcorn:\n text: popcorn\n orange peel:\n text: orange peel\n rosebud stomp:\n text: rosebud stomp\n Santa-Fe texture:\n text: Santa-Fe texture\n skip trowel:\n text: skip trowel\n smooth:\n text: smooth\n stomp knockdown:\n text: stomp knockdown\n swirl:\n text: swirl\n\nURI: CeilTypeEnum
"},{"location":"CeilTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cathedral None dropped None concave None barrel-shaped None coffered None cove None stretched None"},{"location":"CeilTypeEnum/#slots","title":"Slots","text":"Name Description ceil_type The type of ceiling according to the ceiling's appearance or construction"},{"location":"CeilTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CeilTypeEnum/#schema-source","title":"Schema Source","text":"name: ceil_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cathedral:\n text: cathedral\n dropped:\n text: dropped\n concave:\n text: concave\n barrel-shaped:\n text: barrel-shaped\n coffered:\n text: coffered\n cove:\n text: cove\n stretched:\n text: stretched\n\nURI: ChemicalConversionCategoryEnum
"},{"location":"ChemicalConversionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description addition None substitution None acid_base None reduction_oxidation None combustion None decomposition None protease_cleavage OBI:0600056 an enzymatic cleavage which relies on an enzyme with protease activity to act..."},{"location":"ChemicalConversionCategoryEnum/#slots","title":"Slots","text":"Name Description chemical_conversion_category The type of chemical conversion process"},{"location":"ChemicalConversionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalConversionCategoryEnum/#schema-source","title":"Schema Source","text":"name: ChemicalConversionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n addition:\n text: addition\n substitution:\n text: substitution\n acid_base:\n text: acid_base\n reduction_oxidation:\n text: reduction_oxidation\n combustion:\n text: combustion\n decomposition:\n text: decomposition\n protease_cleavage:\n text: protease_cleavage\n description: an enzymatic cleavage which relies on an enzyme with protease activity\n to act on proteins and to produce polypeptides (protein fragments).\n meaning: OBI:0600056\n\nA process that results in the interconversion of chemical species by a reaction to transform the reagents into products.
__
URI: nmdc:ChemicalConversionProcess
classDiagram\n class ChemicalConversionProcess\n click ChemicalConversionProcess href \"../ChemicalConversionProcess\"\n MaterialProcessing <|-- ChemicalConversionProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n ChemicalConversionProcess : alternative_identifiers\n\n ChemicalConversionProcess : chemical_conversion_category\n\n ChemicalConversionProcess --> \"0..1\" ChemicalConversionCategoryEnum : chemical_conversion_category\n click ChemicalConversionCategoryEnum href \"../ChemicalConversionCategoryEnum\"\n\n ChemicalConversionProcess : description\n\n ChemicalConversionProcess : duration\n\n ChemicalConversionProcess --> \"0..1\" QuantityValue : duration\n click QuantityValue href \"../QuantityValue\"\n\n ChemicalConversionProcess : end_date\n\n ChemicalConversionProcess : has_failure_categorization\n\n ChemicalConversionProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ChemicalConversionProcess : has_input\n\n ChemicalConversionProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n ChemicalConversionProcess : has_output\n\n ChemicalConversionProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n ChemicalConversionProcess : id\n\n ChemicalConversionProcess : instrument_used\n\n ChemicalConversionProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n ChemicalConversionProcess : name\n\n ChemicalConversionProcess : processing_institution\n\n ChemicalConversionProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ChemicalConversionProcess : protocol_link\n\n ChemicalConversionProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ChemicalConversionProcess : qc_comment\n\n ChemicalConversionProcess : qc_status\n\n ChemicalConversionProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ChemicalConversionProcess : start_date\n\n ChemicalConversionProcess : substances_used\n\n ChemicalConversionProcess --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n ChemicalConversionProcess : substances_volume\n\n ChemicalConversionProcess --> \"0..1\" QuantityValue : substances_volume\n click QuantityValue href \"../QuantityValue\"\n\n ChemicalConversionProcess : temperature\n\n ChemicalConversionProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n ChemicalConversionProcess : type\n\n\n\nname: ChemicalConversionProcess\ndescription: 'A process that results in the interconversion of chemical species by\n a reaction to transform the reagents into products.\n\n '\ncomments:\n- The values of both has_reagents slot and has_input slot are considered the reagents\n of a chemical process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical reaction\nexact_mappings:\n- MISO:0000001\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- chemical_conversion_category\n- duration\n- temperature\n- substances_used\n- substances_volume\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ChemicalConversionProcess\n\nname: ChemicalConversionProcess\ndescription: 'A process that results in the interconversion of chemical species by\n a reaction to transform the reagents into products.\n\n '\ncomments:\n- The values of both has_reagents slot and has_input slot are considered the reagents\n of a chemical process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical reaction\nexact_mappings:\n- MISO:0000001\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n chemical_conversion_category:\n name: chemical_conversion_category\n description: The type of chemical conversion process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chemical_conversion_category\n owner: ChemicalConversionProcess\n domain_of:\n - ChemicalConversionProcess\n range: ChemicalConversionCategoryEnum\n duration:\n name: duration\n description: The elapsed time of an activity.\n examples:\n - value: JsonObj(has_numeric_value=2, has_unit='hours')\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: duration\n owner: ChemicalConversionProcess\n domain_of:\n - MixingProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: QuantityValue\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: ChemicalConversionProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n substances_used:\n name: substances_used\n description: The substances that are combined to enable a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: ChemicalConversionProcess\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n substances_volume:\n name: substances_volume\n description: The volume of the combined substances that was included in a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_volume\n owner: ChemicalConversionProcess\n domain_of:\n - ChemicalConversionProcess\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: ChemicalConversionProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ChemicalConversionProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ChemicalConversionProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chcpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChemicalConversionProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChemicalConversionProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ChemicalConversionProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ChemicalConversionProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ChemicalConversionProcess\n\nAn atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states. A chemical entity is a physical entity that pertains to chemistry or biochemistry.
URI: nmdc:ChemicalEntity
classDiagram\n class ChemicalEntity\n click ChemicalEntity href \"../ChemicalEntity\"\n OntologyClass <|-- ChemicalEntity\n click OntologyClass href \"../OntologyClass\"\n\n\n\n ChemicalEntity : alternative_identifiers\n\n ChemicalEntity : alternative_names\n\n ChemicalEntity : chemical_formula\n\n ChemicalEntity : definition\n\n ChemicalEntity : description\n\n ChemicalEntity : id\n\n ChemicalEntity : name\n\n ChemicalEntity : relations\n\n ChemicalEntity --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n ChemicalEntity : type\n\n\n\nInstances of this class should have identifiers with one of the following prefixes:
CHEBI
MS
name: ChemicalEntity\nid_prefixes:\n- CHEBI\n- MS\ndescription: An atom or molecule that can be represented with a chemical formula.\n Include lipids, glycans, natural products, drugs. There may be different terms for\n distinct acid-base forms, protonation states. A chemical entity is a physical entity\n that pertains to chemistry or biochemistry.\ndeprecated: true; as of Jan 2025, NMDC only needs a handful of chemicals and its use\n cases can be served via an enumeration rather than supporting a full class.\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nslots:\n- chemical_formula\nclass_uri: nmdc:ChemicalEntity\n\nname: ChemicalEntity\nid_prefixes:\n- CHEBI\n- MS\ndescription: An atom or molecule that can be represented with a chemical formula.\n Include lipids, glycans, natural products, drugs. There may be different terms for\n distinct acid-base forms, protonation states. A chemical entity is a physical entity\n that pertains to chemistry or biochemistry.\ndeprecated: true; as of Jan 2025, NMDC only needs a handful of chemicals and its use\n cases can be served via an enumeration rather than supporting a full class.\ncomments:\n- As with the parent OntologyClass, we will not assign an nmdc id pattern or typecode\n to this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html\naliases:\n- metabolite\n- chemical substance\n- chemical compound\n- chemical\nexact_mappings:\n- biolink:ChemicalSubstance\nis_a: OntologyClass\nattributes:\n chemical_formula:\n name: chemical_formula\n description: A generic grouping for molecular formulae and empirical formulae\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chemical_formula\n owner: ChemicalEntity\n domain_of:\n - ChemicalEntity\n range: string\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: ChemicalEntity\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: ChemicalEntity\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: ChemicalEntity\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ChemicalEntity\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChemicalEntity\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChemicalEntity\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ChemicalEntity\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ChemicalEntity\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ChemicalEntity\n\nURI: ChemicalEntityEnum
"},{"location":"ChemicalEntityEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description acetonitrile CHEBI:38472 alphaLP MS:1001303 A serine protease that hydrolyzes peptide bonds at the C-terminus of threonin... ammonium_acetate CHEBI:62947 ammonium_bicarbonate CHEBI:184335 Arg-C CHEBI:157791 A cysteine protease that hydrolyzes peptide, ester, and amide bonds at the C-... Asp-N MS:1001304 A zinc metalloendopeptidase that hydrolyzes peptide bonds at the N-terminus o... chloroform CHEBI:35255 chymotrypsin MS:1001306 A serine protease that hydrolyzes peptide bonds at the C-terminus of tryptoph... formic_acid CHEBI:30751 A carboxylic acid that is the simplest aliphatic carboxylic acid, comprising ... glucose CHEBI:17234 Generally considered the most abundant monosaccharide in nature Glu-C None A serine protease that hydrolyzes peptide and ester bonds at the C-terminus o... isopropyl_alcohol CHEBI:17824 Lys-C MS:1001309 A serine protease that hydrolyzes peptide, ester, and amide bonds at the C-te... Lys-N MS:1003093 A metalloendopeptidase that hydrolyzes peptide bonds at the C-terminus of lys... methanol CHEBI:17790 trypsin CHEBI:9765 A serine protease that hydrolyzes peptide bonds at the C-terminus of arginine... water CHEBI:15377 Any form of water used in an experiment including deionized water, distilled ..."},{"location":"ChemicalEntityEnum/#slots","title":"Slots","text":"Name Description known_as The substance from which a portion was taken"},{"location":"ChemicalEntityEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChemicalEntityEnum/#schema-source","title":"Schema Source","text":"name: ChemicalEntityEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n acetonitrile:\n text: acetonitrile\n meaning: CHEBI:38472\n alphaLP:\n text: alphaLP\n description: A serine protease that hydrolyzes peptide bonds at the C-terminus\n of threonine, alanine, serine, and valine.\n meaning: MS:1001303\n ammonium_acetate:\n text: ammonium_acetate\n meaning: CHEBI:62947\n ammonium_bicarbonate:\n text: ammonium_bicarbonate\n meaning: CHEBI:184335\n Arg-C:\n text: Arg-C\n description: A cysteine protease that hydrolyzes peptide, ester, and amide bonds\n at the C-terminus of arginine and with lower efficiency, lysine.\n meaning: CHEBI:157791\n Asp-N:\n text: Asp-N\n description: A zinc metalloendopeptidase that hydrolyzes peptide bonds at the\n N-terminus of aspartic acid.\n meaning: MS:1001304\n chloroform:\n text: chloroform\n meaning: CHEBI:35255\n chymotrypsin:\n text: chymotrypsin\n description: A serine protease that hydrolyzes peptide bonds at the C-terminus\n of tryptophan, leucine, tyrosine, and phenylalanine.\n meaning: MS:1001306\n formic_acid:\n text: formic_acid\n description: A carboxylic acid that is the simplest aliphatic carboxylic acid,\n comprising a hydrogen atom joined to the methyl group of methanol.\n meaning: CHEBI:30751\n glucose:\n text: glucose\n description: Generally considered the most abundant monosaccharide in nature.\n meaning: CHEBI:17234\n Glu-C:\n text: Glu-C\n description: A serine protease that hydrolyzes peptide and ester bonds at the\n C-terminus of aspartic acid or glutamic acid.\n isopropyl_alcohol:\n text: isopropyl_alcohol\n meaning: CHEBI:17824\n Lys-C:\n text: Lys-C\n description: A serine protease that hydrolyzes peptide, ester, and amide bonds\n at the C-terminus of lysine.\n meaning: MS:1001309\n Lys-N:\n text: Lys-N\n description: A metalloendopeptidase that hydrolyzes peptide bonds at the C-terminus\n of lysine.\n meaning: MS:1003093\n methanol:\n text: methanol\n meaning: CHEBI:17790\n trypsin:\n text: trypsin\n description: A serine protease that hydrolyzes peptide bonds at the C-terminus\n of arginine and lysine.\n meaning: CHEBI:9765\n water:\n text: water\n description: Any form of water used in an experiment including deionized water,\n distilled water, and ultrapure water. Protocol or materials and methods should\n be consulted for exact type of water used in an experiment.\n meaning: CHEBI:15377\n\nURI: ChromatographicCategoryEnum
"},{"location":"ChromatographicCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description liquid_chromatography None gas_chromatography None solid_phase_extraction None"},{"location":"ChromatographicCategoryEnum/#slots","title":"Slots","text":"Name Description chromatographic_category The type of chromatography used in a process"},{"location":"ChromatographicCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ChromatographicCategoryEnum/#schema-source","title":"Schema Source","text":"name: ChromatographicCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n liquid_chromatography:\n text: liquid_chromatography\n aliases:\n - LC\n gas_chromatography:\n text: gas_chromatography\n aliases:\n - GC\n solid_phase_extraction:\n text: solid_phase_extraction\n aliases:\n - SPE\n\nThe process of using a selective partitioning of the analyte or interferent between two immiscible phases.
URI: nmdc:ChromatographicSeparationProcess
classDiagram\n class ChromatographicSeparationProcess\n click ChromatographicSeparationProcess href \"../ChromatographicSeparationProcess\"\n MaterialProcessing <|-- ChromatographicSeparationProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n ChromatographicSeparationProcess : alternative_identifiers\n\n ChromatographicSeparationProcess : chromatographic_category\n\n ChromatographicSeparationProcess --> \"0..1\" ChromatographicCategoryEnum : chromatographic_category\n click ChromatographicCategoryEnum href \"../ChromatographicCategoryEnum\"\n\n ChromatographicSeparationProcess : description\n\n ChromatographicSeparationProcess : end_date\n\n ChromatographicSeparationProcess : has_failure_categorization\n\n ChromatographicSeparationProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ChromatographicSeparationProcess : has_input\n\n ChromatographicSeparationProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n ChromatographicSeparationProcess : has_output\n\n ChromatographicSeparationProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n ChromatographicSeparationProcess : id\n\n ChromatographicSeparationProcess : instrument_used\n\n ChromatographicSeparationProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n ChromatographicSeparationProcess : name\n\n ChromatographicSeparationProcess : ordered_mobile_phases\n\n ChromatographicSeparationProcess --> \"*\" MobilePhaseSegment : ordered_mobile_phases\n click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n ChromatographicSeparationProcess : processing_institution\n\n ChromatographicSeparationProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ChromatographicSeparationProcess : protocol_link\n\n ChromatographicSeparationProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ChromatographicSeparationProcess : qc_comment\n\n ChromatographicSeparationProcess : qc_status\n\n ChromatographicSeparationProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ChromatographicSeparationProcess : start_date\n\n ChromatographicSeparationProcess : stationary_phase\n\n ChromatographicSeparationProcess --> \"0..1\" StationaryPhaseEnum : stationary_phase\n click StationaryPhaseEnum href \"../StationaryPhaseEnum\"\n\n ChromatographicSeparationProcess : temperature\n\n ChromatographicSeparationProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n ChromatographicSeparationProcess : type\n\n\n\nname: ChromatographicSeparationProcess\ndescription: The process of using a selective partitioning of the analyte or interferent\n between two immiscible phases.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- chromatographic_category\n- ordered_mobile_phases\n- stationary_phase\n- temperature\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ChromatographicSeparationProcess\n\nname: ChromatographicSeparationProcess\ndescription: The process of using a selective partitioning of the analyte or interferent\n between two immiscible phases.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n chromatographic_category:\n name: chromatographic_category\n description: The type of chromatography used in a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chromatographic_category\n owner: ChromatographicSeparationProcess\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: ChromatographicCategoryEnum\n ordered_mobile_phases:\n name: ordered_mobile_phases\n description: The solution(s) that moves through a chromatography column.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n list_elements_ordered: true\n alias: ordered_mobile_phases\n owner: ChromatographicSeparationProcess\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: MobilePhaseSegment\n multivalued: true\n inlined: true\n inlined_as_list: true\n stationary_phase:\n name: stationary_phase\n description: The material the stationary phase is comprised of used in chromatography.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: stationary_phase\n owner: ChromatographicSeparationProcess\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: StationaryPhaseEnum\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: ChromatographicSeparationProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: ChromatographicSeparationProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ChromatographicSeparationProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ChromatographicSeparationProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:cspro-{id_shoulder}-{id_blade}$'\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChromatographicSeparationProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChromatographicSeparationProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ChromatographicSeparationProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ChromatographicSeparationProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ChromatographicSeparationProcess\n\nA set of parameters that define and control the actions of a chromatography process.
URI: nmdc:ChromatographyConfiguration
classDiagram\n class ChromatographyConfiguration\n click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n Configuration <|-- ChromatographyConfiguration\n click Configuration href \"../Configuration\"\n\n\n\n ChromatographyConfiguration : alternative_identifiers\n\n ChromatographyConfiguration : chromatographic_category\n\n ChromatographyConfiguration --> \"0..1\" ChromatographicCategoryEnum : chromatographic_category\n click ChromatographicCategoryEnum href \"../ChromatographicCategoryEnum\"\n\n ChromatographyConfiguration : description\n\n ChromatographyConfiguration : id\n\n ChromatographyConfiguration : name\n\n ChromatographyConfiguration : ordered_mobile_phases\n\n ChromatographyConfiguration --> \"*\" MobilePhaseSegment : ordered_mobile_phases\n click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n ChromatographyConfiguration : stationary_phase\n\n ChromatographyConfiguration --> \"0..1\" StationaryPhaseEnum : stationary_phase\n click StationaryPhaseEnum href \"../StationaryPhaseEnum\"\n\n ChromatographyConfiguration : temperature\n\n ChromatographyConfiguration --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n ChromatographyConfiguration : type\n\n\n\nname: ChromatographyConfiguration\ndescription: A set of parameters that define and control the actions of a chromatography\n process.\nnotes:\n- This class is intended to represent a chromatography method file associated with\n a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslots:\n- chromatographic_category\n- ordered_mobile_phases\n- stationary_phase\n- temperature\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ChromatographyConfiguration\n\nname: ChromatographyConfiguration\ndescription: A set of parameters that define and control the actions of a chromatography\n process.\nnotes:\n- This class is intended to represent a chromatography method file associated with\n a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n chromatographic_category:\n name: chromatographic_category\n description: The type of chromatography used in a process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: chromatographic_category\n owner: ChromatographyConfiguration\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: ChromatographicCategoryEnum\n ordered_mobile_phases:\n name: ordered_mobile_phases\n description: The solution(s) that moves through a chromatography column.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n list_elements_ordered: true\n alias: ordered_mobile_phases\n owner: ChromatographyConfiguration\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: MobilePhaseSegment\n multivalued: true\n inlined: true\n inlined_as_list: true\n stationary_phase:\n name: stationary_phase\n description: The material the stationary phase is comprised of used in chromatography.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: stationary_phase\n owner: ChromatographyConfiguration\n domain_of:\n - ChromatographyConfiguration\n - ChromatographicSeparationProcess\n range: StationaryPhaseEnum\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: ChromatographyConfiguration\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ChromatographyConfiguration\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ChromatographyConfiguration\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n required: true\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ChromatographyConfiguration\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n required: true\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ChromatographyConfiguration\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ChromatographyConfiguration\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ChromatographyConfiguration\n\nURI: nmdc:CollectingBiosamplesFromSite
classDiagram\n class CollectingBiosamplesFromSite\n click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n PlannedProcess <|-- CollectingBiosamplesFromSite\n click PlannedProcess href \"../PlannedProcess\"\n\n\n\n CollectingBiosamplesFromSite : alternative_identifiers\n\n CollectingBiosamplesFromSite : description\n\n CollectingBiosamplesFromSite : end_date\n\n CollectingBiosamplesFromSite : has_failure_categorization\n\n CollectingBiosamplesFromSite --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n CollectingBiosamplesFromSite : has_input\n\n CollectingBiosamplesFromSite --> \"1..*\" Site : has_input\n click Site href \"../Site\"\n\n CollectingBiosamplesFromSite : has_output\n\n CollectingBiosamplesFromSite --> \"1..*\" Biosample : has_output\n click Biosample href \"../Biosample\"\n\n CollectingBiosamplesFromSite : id\n\n CollectingBiosamplesFromSite : name\n\n CollectingBiosamplesFromSite : processing_institution\n\n CollectingBiosamplesFromSite --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n CollectingBiosamplesFromSite : protocol_link\n\n CollectingBiosamplesFromSite --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n CollectingBiosamplesFromSite : qc_comment\n\n CollectingBiosamplesFromSite : qc_status\n\n CollectingBiosamplesFromSite --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n CollectingBiosamplesFromSite : start_date\n\n CollectingBiosamplesFromSite : type\n\n\n\nname: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n has_input:\n name: has_input\n range: Site\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: Biosample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:CollectingBiosamplesFromSite\n\nname: CollectingBiosamplesFromSite\ntitle: Collecting Biosamples From Site\ncomments:\n- this illustrates implementing a Biosample relation with a process class\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- OBI:0000744\nis_a: PlannedProcess\nslot_usage:\n has_input:\n name: has_input\n range: Site\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: Biosample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: Site\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(frsite|site)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: Biosample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: CollectingBiosamplesFromSite\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:clsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: CollectingBiosamplesFromSite\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: CollectingBiosamplesFromSite\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: CollectingBiosamplesFromSite\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: CollectingBiosamplesFromSite\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:CollectingBiosamplesFromSite\n\nA set of parameters that define the actions of a process and is shared among multiple instances of the process.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:Configuration
classDiagram\n class Configuration\n click Configuration href \"../Configuration\"\n InformationObject <|-- Configuration\n click InformationObject href \"../InformationObject\"\n\n\n Configuration <|-- MassSpectrometryConfiguration\n click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n Configuration <|-- ChromatographyConfiguration\n click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n\n\n\n Configuration : alternative_identifiers\n\n Configuration : description\n\n Configuration : id\n\n Configuration : name\n\n Configuration : type\n\n\n\nname: Configuration\ndescription: A set of parameters that define the actions of a process and is shared\n among multiple instances of the process.\nnotes:\n- This class is intended to represent the parameters within a method file (or similar)\n that control a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nabstract: true\nclass_uri: nmdc:Configuration\n\nname: Configuration\ndescription: A set of parameters that define the actions of a process and is shared\n among multiple instances of the process.\nnotes:\n- This class is intended to represent the parameters within a method file (or similar)\n that control a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Configuration\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Configuration\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Configuration\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Configuration\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Configuration\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Configuration\n\nThe permitted types of containers used in processing metabolomic samples.
URI: ContainerCategoryEnum
"},{"location":"ContainerCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description v-bottom_conical_tube None falcon_tube None"},{"location":"ContainerCategoryEnum/#slots","title":"Slots","text":"Name Description contained_in A type of container"},{"location":"ContainerCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ContainerCategoryEnum/#schema-source","title":"Schema Source","text":"name: ContainerCategoryEnum\ndescription: The permitted types of containers used in processing metabolomic samples.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\npermissible_values:\n v-bottom_conical_tube:\n text: v-bottom_conical_tube\n falcon_tube:\n text: falcon_tube\n\nA controlled term or class from an ontology, requiring the presence of term with an id
URI: nmdc:ControlledIdentifiedTermValue
classDiagram\n class ControlledIdentifiedTermValue\n click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n ControlledTermValue <|-- ControlledIdentifiedTermValue\n click ControlledTermValue href \"../ControlledTermValue\"\n\n\n\n ControlledIdentifiedTermValue : has_raw_value\n\n ControlledIdentifiedTermValue : term\n\n ControlledIdentifiedTermValue --> \"1\" OntologyClass : term\n click OntologyClass href \"../OntologyClass\"\n\n ControlledIdentifiedTermValue : type\n\n\n\nname: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n term:\n name: term\n required: true\nclass_uri: nmdc:ControlledIdentifiedTermValue\n\nname: ControlledIdentifiedTermValue\ndescription: A controlled term or class from an ontology, requiring the presence of\n term with an id\nnotes:\n- To be used for slots like env_broad_scale\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: ControlledTermValue\nslot_usage:\n term:\n name: term\n required: true\nattributes:\n term:\n name: term\n description: pointer to an ontology class\n notes:\n - 'removed ''slot_uri: rdf:type'''\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: term\n owner: ControlledIdentifiedTermValue\n domain_of:\n - ControlledTermValue\n range: OntologyClass\n required: true\n inlined: true\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: ControlledIdentifiedTermValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ControlledIdentifiedTermValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ControlledIdentifiedTermValue\n\nA controlled term or class from an ontology
URI: nmdc:ControlledTermValue
classDiagram\n class ControlledTermValue\n click ControlledTermValue href \"../ControlledTermValue\"\n AttributeValue <|-- ControlledTermValue\n click AttributeValue href \"../AttributeValue\"\n\n\n ControlledTermValue <|-- ControlledIdentifiedTermValue\n click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n\n\n ControlledTermValue : has_raw_value\n\n ControlledTermValue : term\n\n ControlledTermValue --> \"0..1\" OntologyClass : term\n click OntologyClass href \"../OntologyClass\"\n\n ControlledTermValue : type\n\n\n\nname: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- term\nclass_uri: nmdc:ControlledTermValue\n\nname: ControlledTermValue\ndescription: A controlled term or class from an ontology\ntodos:\n- add fields for ontology, branch\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n term:\n name: term\n description: pointer to an ontology class\n notes:\n - 'removed ''slot_uri: rdf:type'''\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: term\n owner: ControlledTermValue\n domain_of:\n - ControlledTermValue\n range: OntologyClass\n inlined: true\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: ControlledTermValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ControlledTermValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ControlledTermValue\n\nThis class supports binding associated researchers to studies. There will be at least a slot for a CRediT Contributor Role and for a person value. Specifically see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0
URI: prov:Association
classDiagram\n class CreditAssociation\n click CreditAssociation href \"../CreditAssociation\"\n\n CreditAssociation : applied_roles\n\n CreditAssociation --> \"1..*\" CreditEnum : applied_roles\n click CreditEnum href \"../CreditEnum\"\n\n CreditAssociation : applies_to_person\n\n CreditAssociation --> \"1\" PersonValue : applies_to_person\n click PersonValue href \"../PersonValue\"\n\n CreditAssociation : type\n\n\n\nname: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n will be at least a slot for a CRediT Contributor Role and for a person value. Specifically\n see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://casrai.org/credit/\naliases:\n- study role\n- credit table\n- associated researchers\nslots:\n- applies_to_person\n- applied_roles\n- type\nclass_uri: prov:Association\n\nname: CreditAssociation\ndescription: This class supports binding associated researchers to studies. There\n will be at least a slot for a CRediT Contributor Role and for a person value. Specifically\n see the associated researchers tab on the NMDC_SampleMetadata-V4_CommentsForUpdates\n at https://docs.google.com/spreadsheets/d/1INlBo5eoqn2efn4H2P2i8rwRBtnbDVTqXrochJEAPko/edit#gid=0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://casrai.org/credit/\naliases:\n- study role\n- credit table\n- associated researchers\nattributes:\n applies_to_person:\n name: applies_to_person\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: applies_to_person\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: PersonValue\n required: true\n applied_roles:\n name: applied_roles\n annotations:\n tooltip:\n tag: tooltip\n value: 'Identify all CRediT roles associated with this contributor. CRediT\n Information: https://info.orcid.org/credit-for-research-contribution ; CRediT:\n https://credit.niso.org/'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: applied_roles\n owner: CreditAssociation\n domain_of:\n - CreditAssociation\n range: CreditEnum\n required: true\n multivalued: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: CreditAssociation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: prov:Association\n\nURI: CreditEnum
"},{"location":"CreditEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Conceptualization None Conceptualization Data curation None Data curation Formal Analysis None Formal Analysis Funding acquisition None Funding acquisition Investigation None Investigation Methodology None Methodology Project administration None Project administration Resources None Resources Software None Software Supervision None Supervision Validation None Validation Visualization None Visualization Writing original draft None Writing \u2013 original draft Writing review and editing None Writing \u2013 review & editing Principal Investigator OBI:0000103 principal investigator role Submitter EFO:0001741 the person(s) who enter study and biosample metadata into the NMDC submission..."},{"location":"CreditEnum/#slots","title":"Slots","text":"Name Description applied_roles"},{"location":"CreditEnum/#comments","title":"Comments","text":"name: CreditEnum\ncomments:\n- CreditEnums come from https://casrai.org/credit/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Conceptualization:\n text: Conceptualization\n description: Conceptualization\n Data curation:\n text: Data curation\n description: Data curation\n Formal Analysis:\n text: Formal Analysis\n description: Formal Analysis\n Funding acquisition:\n text: Funding acquisition\n description: Funding acquisition\n Investigation:\n text: Investigation\n description: Investigation\n Methodology:\n text: Methodology\n description: Methodology\n Project administration:\n text: Project administration\n description: Project administration\n Resources:\n text: Resources\n description: Resources\n Software:\n text: Software\n description: Software\n Supervision:\n text: Supervision\n description: Supervision\n Validation:\n text: Validation\n description: Validation\n Visualization:\n text: Visualization\n description: Visualization\n Writing original draft:\n text: Writing original draft\n description: Writing \u2013 original draft\n Writing review and editing:\n text: Writing review and editing\n description: Writing \u2013 review & editing\n Principal Investigator:\n text: Principal Investigator\n description: principal investigator role\n meaning: OBI:0000103\n Submitter:\n text: Submitter\n description: the person(s) who enter study and biosample metadata into the NMDC\n submission portal\n meaning: EFO:0001741\n\nURI: CurLandUseEnum
"},{"location":"CurLandUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description badlands None cities None conifers None crop trees None farmstead None gravel None hardwoods None hayland None horticultural plants None industrial areas None intermixed hardwood and conifers None marshlands None meadows None mines/quarries None mudflats None oil waste areas None pastureland None permanent snow or ice None rainforest None rangeland None roads/railroads None rock None row crops None saline seeps None salt flats None sand None shrub crops None shrub land None small grains None successional shrub land None swamp None tropical None tundra None vegetable crops None vine crops None"},{"location":"CurLandUseEnum/#slots","title":"Slots","text":"Name Description cur_land_use Present state of sample site"},{"location":"CurLandUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"CurLandUseEnum/#schema-source","title":"Schema Source","text":"name: cur_land_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n badlands:\n text: badlands\n cities:\n text: cities\n conifers:\n text: conifers\n annotations:\n originally:\n tag: originally\n value: conifers (e.g. pine,spruce,fir,cypress)\n examples:\n - value: cypress\n - value: fir\n - value: pine\n - value: spruce\n crop trees:\n text: crop trees\n annotations:\n originally:\n tag: originally\n value: crop trees (nuts,fruit,christmas trees,nursery trees)\n examples:\n - value: christmas trees\n - value: fruit\n - value: nursery trees\n - value: nuts\n farmstead:\n text: farmstead\n gravel:\n text: gravel\n hardwoods:\n text: hardwoods\n annotations:\n originally:\n tag: originally\n value: hardwoods (e.g. oak,hickory,elm,aspen)\n examples:\n - value: aspen\n - value: elm\n - value: hickory\n - value: oak\n hayland:\n text: hayland\n horticultural plants:\n text: horticultural plants\n annotations:\n originally:\n tag: originally\n value: horticultural plants (e.g. tulips)\n examples:\n - value: tulips\n industrial areas:\n text: industrial areas\n intermixed hardwood and conifers:\n text: intermixed hardwood and conifers\n marshlands:\n text: marshlands\n annotations:\n originally:\n tag: originally\n value: marshlands (grass,sedges,rushes)\n examples:\n - value: grass\n - value: rushes\n - value: sedgees\n meadows:\n text: meadows\n annotations:\n originally:\n tag: originally\n value: meadows (grasses,alfalfa,fescue,bromegrass,timothy)\n examples:\n - value: alfalfa\n - value: bromegrass\n - value: fescue\n - value: grasses\n - value: timothy\n mines/quarries:\n text: mines/quarries\n mudflats:\n text: mudflats\n oil waste areas:\n text: oil waste areas\n pastureland:\n text: pastureland\n annotations:\n originally:\n tag: originally\n value: pastureland (grasslands used for livestock grazing)\n comments:\n - grasslands used for livestock grazing\n permanent snow or ice:\n text: permanent snow or ice\n rainforest:\n text: rainforest\n annotations:\n originally:\n tag: originally\n value: rainforest (evergreen forest receiving greater than 406 cm annual rainfall)\n comments:\n - evergreen forest receiving greater than 406 cm annual rainfall\n rangeland:\n text: rangeland\n roads/railroads:\n text: roads/railroads\n rock:\n text: rock\n row crops:\n text: row crops\n saline seeps:\n text: saline seeps\n salt flats:\n text: salt flats\n sand:\n text: sand\n shrub crops:\n text: shrub crops\n annotations:\n originally:\n tag: originally\n value: shrub crops (blueberries,nursery ornamentals,filberts)\n examples:\n - value: blueberries\n - value: filberts\n - value: nursery ornamentals\n shrub land:\n text: shrub land\n annotations:\n originally:\n tag: originally\n value: shrub land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)\n examples:\n - value: creosote bush\n - value: eucalyptus\n - value: mesquite\n - value: sage-brush\n - value: shrub oak\n small grains:\n text: small grains\n successional shrub land:\n text: successional shrub land\n annotations:\n originally:\n tag: originally\n value: successional shrub land (tree saplings,hazels,sumacs,chokecherry,shrub\n dogwoods,blackberries)\n examples:\n - value: blackberries\n - value: chokecherry\n - value: hazels\n - value: shrub dogwoods\n - value: sumacs\n - value: tree saplings\n swamp:\n text: swamp\n annotations:\n originally:\n tag: originally\n value: swamp (permanent or semi-permanent water body dominated by woody plants)\n comments:\n - permanent or semi-permanent water body dominated by woody plants\n tropical:\n text: tropical\n annotations:\n originally:\n tag: originally\n value: tropical (e.g. mangrove,palms)\n examples:\n - value: mangrove\n - value: palms\n tundra:\n text: tundra\n annotations:\n originally:\n tag: originally\n value: tundra (mosses,lichens)\n examples:\n - value: lichens\n - value: mosses\n vegetable crops:\n text: vegetable crops\n vine crops:\n text: vine crops\n annotations:\n originally:\n tag: originally\n value: vine crops (grapes)\n examples:\n - value: grapes\n\na compact URI
URI: xsd:string
base: Curie
uri: xsd:string
repr: str
URI: DNASampleFormatEnum
"},{"location":"DNASampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"DNASampleFormatEnum/#slots","title":"Slots","text":"Name Description dna_sample_format Solution in which the DNA sample has been suspended"},{"location":"DNASampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DNASampleFormatEnum/#schema-source","title":"Schema Source","text":"name: DNASampleFormatEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 10 mM Tris-HCl:\n text: 10 mM Tris-HCl\n DNAStable:\n text: DNAStable\n Ethanol:\n text: Ethanol\n Low EDTA TE:\n text: Low EDTA TE\n MDA reaction buffer:\n text: MDA reaction buffer\n PBS:\n text: PBS\n Pellet:\n text: Pellet\n RNAStable:\n text: RNAStable\n TE:\n text: TE\n Water:\n text: Water\n Gentegra-DNA:\n text: Gentegra-DNA\n Gentegra-RNA:\n text: Gentegra-RNA\n\nURI: DataCategoryEnum
"},{"location":"DataCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description instrument_data None Data generated by a DataGeneration PlannedProcess processed_data None Data generated by a WorkflowExecution PlannedProcess workflow_parameter_data None Data used as input into a workflow providing workflow specification"},{"location":"DataCategoryEnum/#slots","title":"Slots","text":"Name Description data_category The category of the file, such as instrument data from data generation or pro..."},{"location":"DataCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DataCategoryEnum/#schema-source","title":"Schema Source","text":"name: DataCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n instrument_data:\n text: instrument_data\n description: Data generated by a DataGeneration PlannedProcess\n processed_data:\n text: processed_data\n description: Data generated by a WorkflowExecution PlannedProcess\n workflow_parameter_data:\n text: workflow_parameter_data\n description: Data used as input into a workflow providing workflow specification.\n related_mappings:\n - edam.data:0949\n\nThe methods and processes used to generate omics data from a biosample or organism.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:DataGeneration
classDiagram\n class DataGeneration\n click DataGeneration href \"../DataGeneration\"\n PlannedProcess <|-- DataGeneration\n click PlannedProcess href \"../PlannedProcess\"\n\n\n DataGeneration <|-- NucleotideSequencing\n click NucleotideSequencing href \"../NucleotideSequencing\"\n DataGeneration <|-- MassSpectrometry\n click MassSpectrometry href \"../MassSpectrometry\"\n\n\n\n DataGeneration : add_date\n\n DataGeneration : alternative_identifiers\n\n DataGeneration : analyte_category\n\n DataGeneration : associated_studies\n\n DataGeneration --> \"1..*\" Study : associated_studies\n click Study href \"../Study\"\n\n DataGeneration : description\n\n DataGeneration : end_date\n\n DataGeneration : has_failure_categorization\n\n DataGeneration --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n DataGeneration : has_input\n\n DataGeneration --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n DataGeneration : has_output\n\n DataGeneration --> \"*\" DataObject : has_output\n click DataObject href \"../DataObject\"\n\n DataGeneration : id\n\n DataGeneration : instrument_used\n\n DataGeneration --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n DataGeneration : mod_date\n\n DataGeneration : name\n\n DataGeneration : principal_investigator\n\n DataGeneration --> \"0..1\" PersonValue : principal_investigator\n click PersonValue href \"../PersonValue\"\n\n DataGeneration : processing_institution\n\n DataGeneration --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n DataGeneration : protocol_link\n\n DataGeneration --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n DataGeneration : qc_comment\n\n DataGeneration : qc_status\n\n DataGeneration --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n DataGeneration : start_date\n\n DataGeneration : type\n\n\n\nname: DataGeneration\ndescription: The methods and processes used to generate omics data from a biosample\n or organism.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An experiment contains information about a sequencing experiment\n including library and instrument details.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OmicsProcessing\n- assay\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nabstract: true\nslots:\n- add_date\n- analyte_category\n- associated_studies\n- instrument_used\n- mod_date\n- principal_investigator\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n associated_studies:\n name: associated_studies\n range: Study\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: DataObject\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:DataGeneration\n\nname: DataGeneration\ndescription: The methods and processes used to generate omics data from a biosample\n or organism.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An experiment contains information about a sequencing experiment\n including library and instrument details.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OmicsProcessing\n- assay\n- omics assay\n- sequencing project\n- experiment\nbroad_mappings:\n- OBI:0000070\n- ISA:Assay\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n associated_studies:\n name: associated_studies\n range: Study\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: DataObject\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: DataGeneration\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n analyte_category:\n name: analyte_category\n description: \"The type of analyte(s) that were measured in the data generation\\\n \\ process and analyzed\\n in the Workflow Chain\\n\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: analyte_category\n owner: DataGeneration\n domain_of:\n - DataGeneration\n range: string\n required: true\n associated_studies:\n name: associated_studies\n description: The study associated with a resource.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: associated_studies\n owner: DataGeneration\n domain_of:\n - Biosample\n - DataGeneration\n range: Study\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: DataGeneration\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: DataGeneration\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n alias: principal_investigator\n owner: DataGeneration\n domain_of:\n - Study\n - DataGeneration\n range: PersonValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: DataObject\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: DataGeneration\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: DataGeneration\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: DataGeneration\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: DataGeneration\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: DataGeneration\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: DataGeneration\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:DataGeneration\n\nAn object that primarily consists of symbols that represent information. Files, records, and omics data are examples of data objects.
URI: nmdc:DataObject
classDiagram\n class DataObject\n click DataObject href \"../DataObject\"\n InformationObject <|-- DataObject\n click InformationObject href \"../InformationObject\"\n\n\n\n DataObject : alternative_identifiers\n\n DataObject : compression_type\n\n DataObject : data_category\n\n DataObject --> \"0..1\" DataCategoryEnum : data_category\n click DataCategoryEnum href \"../DataCategoryEnum\"\n\n DataObject : data_object_type\n\n DataObject --> \"0..1\" FileTypeEnum : data_object_type\n click FileTypeEnum href \"../FileTypeEnum\"\n\n DataObject : description\n\n DataObject : file_size_bytes\n\n DataObject : id\n\n DataObject : in_manifest\n\n DataObject --> \"*\" Manifest : in_manifest\n click Manifest href \"../Manifest\"\n\n DataObject : insdc_experiment_identifiers\n\n DataObject : md5_checksum\n\n DataObject : name\n\n DataObject : type\n\n DataObject : url\n\n DataObject : was_generated_by\n\n DataObject --> \"0..1\" WorkflowExecution : was_generated_by\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\nname: DataObject\ndescription: An object that primarily consists of symbols that represent information. Files,\n records, and omics data are examples of data objects.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- compression_type\n- data_category\n- data_object_type\n- file_size_bytes\n- insdc_experiment_identifiers\n- md5_checksum\n- url\n- was_generated_by\n- in_manifest\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_generated_by:\n name: was_generated_by\n structured_pattern:\n syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n interpolated: true\nclass_uri: nmdc:DataObject\n\nname: DataObject\ndescription: An object that primarily consists of symbols that represent information. Files,\n records, and omics data are examples of data objects.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_generated_by:\n name: was_generated_by\n structured_pattern:\n syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n interpolated: true\nattributes:\n compression_type:\n name: compression_type\n description: If provided, specifies the compression type\n todos:\n - consider setting the range to an enum\n examples:\n - value: gzip\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: compression_type\n owner: DataObject\n domain_of:\n - DataObject\n range: string\n data_category:\n name: data_category\n description: The category of the file, such as instrument data from data generation\n or processed data from a workflow execution.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: data_category\n owner: DataObject\n domain_of:\n - DataObject\n range: DataCategoryEnum\n data_object_type:\n name: data_object_type\n description: The type of file represented by the data object.\n examples:\n - value: FT ICR-MS Analysis Results\n - value: GC-MS Metabolomics Results\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n data_object_type:\n literal_form: data_object_type\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n alias: data_object_type\n owner: DataObject\n domain_of:\n - DataObject\n range: FileTypeEnum\n file_size_bytes:\n name: file_size_bytes\n description: Size of the file in bytes\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: file_size_bytes\n owner: DataObject\n domain_of:\n - DataObject\n range: bytes\n insdc_experiment_identifiers:\n name: insdc_experiment_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_experiment_identifiers\n owner: DataObject\n domain_of:\n - NucleotideSequencing\n - DataObject\n range: external_identifier\n multivalued: true\n pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n md5_checksum:\n name: md5_checksum\n description: MD5 checksum of file (pre-compressed)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: md5_checksum\n owner: DataObject\n domain_of:\n - DataObject\n range: string\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: url\n owner: DataObject\n domain_of:\n - ImageValue\n - Protocol\n - DataObject\n range: string\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: DataObject\n domain_of:\n - FunctionalAnnotationAggMember\n - FunctionalAnnotation\n - DataObject\n range: WorkflowExecution\n structured_pattern:\n syntax: ^{id_nmdc_prefix}:(wfmag|wfmb|wfmgan|wfmgas|wfmsa|wfmp|wfmt|wfmtan|wfmtas|wfnom|wfrbt|wfrqc)-{id_shoulder}-{id_blade}{id_version}$|^{id_nmdc_prefix}:(omprc|dgms|dgns)-{id_shoulder}-{id_blade}$\n interpolated: true\n any_of:\n - range: WorkflowExecution\n - range: DataGeneration\n in_manifest:\n name: in_manifest\n description: one or more combinations of other DataObjects that can be analyzed\n together\n comments:\n - A DataObject can be part of multiple manifests, for example, a DataObject could\n be part of a manifest for a single run of an instrument and a manifest for technical\n replicates of a single sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: in_manifest\n owner: DataObject\n domain_of:\n - DataObject\n range: Manifest\n multivalued: true\n structured_pattern:\n syntax: ^{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$\n interpolated: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: DataObject\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: DataObject\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n required: true\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: DataObject\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n required: true\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: DataObject\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: DataObject\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:DataObject\n\nAn abstract holder for any set of metadata and data. It does not need to correspond to an actual managed database top level holder class. When translated to JSON-Schema this is the 'root' object. It should contain pointers to other objects of interest. For MongoDB, the lists of objects that Database slots point to correspond to collections.
URI: nmdc:Database
classDiagram\n class Database\n click Database href \"../Database\"\n\n Database : biosample_set\n\n Database --> \"*\" Biosample : biosample_set\n click Biosample href \"../Biosample\"\n\n Database : calibration_set\n\n Database --> \"*\" CalibrationInformation : calibration_set\n click CalibrationInformation href \"../CalibrationInformation\"\n\n Database : collecting_biosamples_from_site_set\n\n Database --> \"*\" CollectingBiosamplesFromSite : collecting_biosamples_from_site_set\n click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n\n Database : configuration_set\n\n Database --> \"*\" Configuration : configuration_set\n click Configuration href \"../Configuration\"\n\n Database : data_generation_set\n\n Database --> \"*\" DataGeneration : data_generation_set\n click DataGeneration href \"../DataGeneration\"\n\n Database : data_object_set\n\n Database --> \"*\" DataObject : data_object_set\n click DataObject href \"../DataObject\"\n\n Database : field_research_site_set\n\n Database --> \"*\" FieldResearchSite : field_research_site_set\n click FieldResearchSite href \"../FieldResearchSite\"\n\n Database : functional_annotation_agg\n\n Database --> \"*\" FunctionalAnnotationAggMember : functional_annotation_agg\n click FunctionalAnnotationAggMember href \"../FunctionalAnnotationAggMember\"\n\n Database : functional_annotation_set\n\n Database --> \"*\" FunctionalAnnotation : functional_annotation_set\n click FunctionalAnnotation href \"../FunctionalAnnotation\"\n\n Database : genome_feature_set\n\n Database --> \"*\" GenomeFeature : genome_feature_set\n click GenomeFeature href \"../GenomeFeature\"\n\n Database : instrument_set\n\n Database --> \"*\" Instrument : instrument_set\n click Instrument href \"../Instrument\"\n\n Database : manifest_set\n\n Database --> \"*\" Manifest : manifest_set\n click Manifest href \"../Manifest\"\n\n Database : material_processing_set\n\n Database --> \"*\" MaterialProcessing : material_processing_set\n click MaterialProcessing href \"../MaterialProcessing\"\n\n Database : processed_sample_set\n\n Database --> \"*\" ProcessedSample : processed_sample_set\n click ProcessedSample href \"../ProcessedSample\"\n\n Database : protocol_execution_set\n\n Database --> \"*\" ProtocolExecution : protocol_execution_set\n click ProtocolExecution href \"../ProtocolExecution\"\n\n Database : storage_process_set\n\n Database --> \"*\" StorageProcess : storage_process_set\n click StorageProcess href \"../StorageProcess\"\n\n Database : study_set\n\n Database --> \"*\" Study : study_set\n click Study href \"../Study\"\n\n Database : workflow_execution_set\n\n Database --> \"*\" WorkflowExecution : workflow_execution_set\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\nname: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n to correspond to an actual managed database top level holder class. When translated\n to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n of interest. For MongoDB, the lists of objects that Database slots point to correspond\n to **collections**.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nslots:\n- biosample_set\n- calibration_set\n- collecting_biosamples_from_site_set\n- configuration_set\n- data_generation_set\n- data_object_set\n- field_research_site_set\n- functional_annotation_agg\n- functional_annotation_set\n- genome_feature_set\n- instrument_set\n- manifest_set\n- material_processing_set\n- processed_sample_set\n- protocol_execution_set\n- storage_process_set\n- study_set\n- workflow_execution_set\nclass_uri: nmdc:Database\ntree_root: true\n\nname: Database\ndescription: An abstract holder for any set of metadata and data. It does not need\n to correspond to an actual managed database top level holder class. When translated\n to JSON-Schema this is the 'root' object. It should contain pointers to other objects\n of interest. For MongoDB, the lists of objects that Database slots point to correspond\n to **collections**.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- NMDC metadata object\nattributes:\n biosample_set:\n name: biosample_set\n description: This property links a database object to the set of samples within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: biosample_set\n owner: Database\n domain_of:\n - Database\n range: Biosample\n multivalued: true\n inlined_as_list: true\n calibration_set:\n name: calibration_set\n description: This property links a database object to the set of calibrations\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: calibration_set\n owner: Database\n domain_of:\n - Database\n range: CalibrationInformation\n multivalued: true\n inlined_as_list: true\n collecting_biosamples_from_site_set:\n name: collecting_biosamples_from_site_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: collecting_biosamples_from_site_set\n owner: Database\n domain_of:\n - Database\n range: CollectingBiosamplesFromSite\n multivalued: true\n inlined_as_list: true\n configuration_set:\n name: configuration_set\n description: This property links a database object to the set of configurations\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: configuration_set\n owner: Database\n domain_of:\n - Database\n range: Configuration\n multivalued: true\n inlined_as_list: true\n data_generation_set:\n name: data_generation_set\n description: This property links a database object to the set of data generations\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: data_generation_set\n owner: Database\n domain_of:\n - Database\n range: DataGeneration\n multivalued: true\n inlined_as_list: true\n data_object_set:\n name: data_object_set\n description: This property links a database object to the set of data objects\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: data_object_set\n owner: Database\n domain_of:\n - Database\n range: DataObject\n multivalued: true\n inlined_as_list: true\n field_research_site_set:\n name: field_research_site_set\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: field_research_site_set\n owner: Database\n domain_of:\n - Database\n range: FieldResearchSite\n multivalued: true\n inlined_as_list: true\n functional_annotation_agg:\n name: functional_annotation_agg\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: functional_annotation_agg\n owner: Database\n domain_of:\n - Database\n range: FunctionalAnnotationAggMember\n multivalued: true\n inlined: true\n inlined_as_list: true\n functional_annotation_set:\n name: functional_annotation_set\n description: This property links a database object to the set of all functional\n annotations\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: functional_annotation_set\n owner: Database\n domain_of:\n - Database\n range: FunctionalAnnotation\n multivalued: true\n inlined_as_list: true\n genome_feature_set:\n name: genome_feature_set\n description: This property links a database object to the set of all features\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: genome_feature_set\n owner: Database\n domain_of:\n - Database\n range: GenomeFeature\n multivalued: true\n inlined_as_list: true\n instrument_set:\n name: instrument_set\n description: This property links a database object to the set of instruments within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: instrument_set\n owner: Database\n domain_of:\n - Database\n range: Instrument\n multivalued: true\n inlined_as_list: true\n manifest_set:\n name: manifest_set\n description: This property links a database object to the set of manifests within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: manifest_set\n owner: Database\n domain_of:\n - Database\n range: Manifest\n multivalued: true\n inlined_as_list: true\n material_processing_set:\n name: material_processing_set\n description: This property links a database object to the set of material processing\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: material_processing_set\n owner: Database\n domain_of:\n - Database\n range: MaterialProcessing\n multivalued: true\n inlined_as_list: true\n processed_sample_set:\n name: processed_sample_set\n description: This property links a database object to the set of processed samples\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: processed_sample_set\n owner: Database\n domain_of:\n - Database\n range: ProcessedSample\n multivalued: true\n inlined_as_list: true\n protocol_execution_set:\n name: protocol_execution_set\n description: This property links a database object to the set of protocol executions\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: protocol_execution_set\n owner: Database\n domain_of:\n - Database\n range: ProtocolExecution\n multivalued: true\n inlined_as_list: true\n storage_process_set:\n name: storage_process_set\n description: This property links a database object to the set of storage processes\n within it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: storage_process_set\n owner: Database\n domain_of:\n - Database\n range: StorageProcess\n multivalued: true\n inlined_as_list: true\n study_set:\n name: study_set\n description: This property links a database object to the set of studies within\n it.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: study_set\n owner: Database\n domain_of:\n - Database\n range: Study\n multivalued: true\n inlined_as_list: true\n workflow_execution_set:\n name: workflow_execution_set\n description: This property links a database object to the set of workflow executions.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n mixins:\n - object_set\n alias: workflow_execution_set\n owner: Database\n domain_of:\n - Database\n range: WorkflowExecution\n multivalued: true\n inlined_as_list: true\nclass_uri: nmdc:Database\ntree_root: true\n\na date (year, month and day) in an idealized calendar
URI: xsd:date
base: XSDDate
uri: xsd:date
repr: str
Either a date or a datetime
URI: linkml:DateOrDatetime
base: str
uri: linkml:DateOrDatetime
repr: str
The combination of a date and time
URI: xsd:dateTime
base: XSDDateTime
uri: xsd:dateTime
repr: str
A real number with arbitrary precision that conforms to the xsd:decimal specification
URI: xsd:decimal
base: Decimal
uri: xsd:decimal
A decimal degree expresses latitude or longitude as decimal fractions.
URI: xsd:decimal
base: float
uri: xsd:decimal
URI: DeposEnvEnum
"},{"location":"DeposEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Continental - Alluvial None Continental - Aeolian None Continental - Fluvial None Continental - Lacustrine None Transitional - Deltaic None Transitional - Tidal None Transitional - Lagoonal None Transitional - Beach None Transitional - Lake None Marine - Shallow None Marine - Deep None Marine - Reef None Other - Evaporite None Other - Glacial None Other - Volcanic None other None"},{"location":"DeposEnvEnum/#slots","title":"Slots","text":"Name Description depos_env Main depositional environment (https://en"},{"location":"DeposEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DeposEnvEnum/#schema-source","title":"Schema Source","text":"name: depos_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Continental - Alluvial:\n text: Continental - Alluvial\n Continental - Aeolian:\n text: Continental - Aeolian\n Continental - Fluvial:\n text: Continental - Fluvial\n Continental - Lacustrine:\n text: Continental - Lacustrine\n Transitional - Deltaic:\n text: Transitional - Deltaic\n Transitional - Tidal:\n text: Transitional - Tidal\n Transitional - Lagoonal:\n text: Transitional - Lagoonal\n Transitional - Beach:\n text: Transitional - Beach\n Transitional - Lake:\n text: Transitional - Lake\n Marine - Shallow:\n text: Marine - Shallow\n Marine - Deep:\n text: Marine - Deep\n Marine - Reef:\n text: Marine - Reef\n Other - Evaporite:\n text: Other - Evaporite\n Other - Glacial:\n text: Other - Glacial\n Other - Volcanic:\n text: Other - Volcanic\n other:\n text: other\n\nA mixing step where a soluble component is mixed with a liquid component.
__
URI: nmdc:DissolvingProcess
classDiagram\n class DissolvingProcess\n click DissolvingProcess href \"../DissolvingProcess\"\n MaterialProcessing <|-- DissolvingProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n DissolvingProcess : alternative_identifiers\n\n DissolvingProcess : description\n\n DissolvingProcess : duration\n\n DissolvingProcess --> \"0..1\" QuantityValue : duration\n click QuantityValue href \"../QuantityValue\"\n\n DissolvingProcess : end_date\n\n DissolvingProcess : has_failure_categorization\n\n DissolvingProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n DissolvingProcess : has_input\n\n DissolvingProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n DissolvingProcess : has_output\n\n DissolvingProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n DissolvingProcess : id\n\n DissolvingProcess : instrument_used\n\n DissolvingProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n DissolvingProcess : name\n\n DissolvingProcess : processing_institution\n\n DissolvingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n DissolvingProcess : protocol_link\n\n DissolvingProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n DissolvingProcess : qc_comment\n\n DissolvingProcess : qc_status\n\n DissolvingProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n DissolvingProcess : start_date\n\n DissolvingProcess : substances_used\n\n DissolvingProcess --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n DissolvingProcess : temperature\n\n DissolvingProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n DissolvingProcess : type\n\n\n\nname: DissolvingProcess\ndescription: 'A mixing step where a soluble component is mixed with a liquid component.\n\n '\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Solubilization\nexact_mappings:\n- CHMO:0002773\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslots:\n- duration\n- temperature\n- substances_used\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:DissolvingProcess\n\nname: DissolvingProcess\ndescription: 'A mixing step where a soluble component is mixed with a liquid component.\n\n '\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Solubilization\nexact_mappings:\n- CHMO:0002773\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-1368-8217\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n duration:\n name: duration\n description: The elapsed time of an activity.\n examples:\n - value: JsonObj(has_numeric_value=2, has_unit='hours')\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: duration\n owner: DissolvingProcess\n domain_of:\n - MixingProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: QuantityValue\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: DissolvingProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n substances_used:\n name: substances_used\n description: The substances that are combined to enable a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: DissolvingProcess\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: DissolvingProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: DissolvingProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: DissolvingProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:dispro-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: DissolvingProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: DissolvingProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: DissolvingProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: DissolvingProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:DissolvingProcess\n\nA centrally registered identifier symbol used to uniquely identify objects given by the International DOI Foundation. The DOI system is particularly used for electronic documents.
URI: nmdc:Doi
classDiagram\n class Doi\n click Doi href \"../Doi\"\n\n Doi : doi_category\n\n Doi --> \"1\" DoiCategoryEnum : doi_category\n click DoiCategoryEnum href \"../DoiCategoryEnum\"\n\n Doi : doi_provider\n\n Doi --> \"0..1\" DoiProviderEnum : doi_provider\n click DoiProviderEnum href \"../DoiProviderEnum\"\n\n Doi : doi_value\n\n Doi : type\n\n\n\nname: Doi\ndescription: A centrally registered identifier symbol used to uniquely identify objects\n given by the International DOI Foundation. The DOI system is particularly used for\n electronic documents.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOIs\n- digital object identifiers\nexact_mappings:\n- OBI:0002110\nslots:\n- doi_value\n- doi_provider\n- doi_category\n- type\nclass_uri: nmdc:Doi\nrules:\n- preconditions:\n slot_conditions:\n doi_category:\n name: doi_category\n any_of:\n - equals_string: dataset_doi\n - equals_string: award_doi\n postconditions:\n slot_conditions:\n doi_provider:\n name: doi_provider\n required: true\n description: If doi_category is a publication_doi, then doi_provider is not required.\n Otherwise, doi_provider is required.\n title: dataset_award_dois_required\n\nname: Doi\ndescription: A centrally registered identifier symbol used to uniquely identify objects\n given by the International DOI Foundation. The DOI system is particularly used for\n electronic documents.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOIs\n- digital object identifiers\nexact_mappings:\n- OBI:0002110\nattributes:\n doi_value:\n name: doi_value\n description: A digital object identifier, which is intended to persistantly identify\n some resource on the web.\n examples:\n - value: doi:10.46936/10.25585/60000880\n description: The DOI links to an electronic document.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - DOI\n - digital object identifier\n exact_mappings:\n - OBI:0002110\n narrow_mappings:\n - edam.data:1188\n rank: 1000\n alias: doi_value\n owner: Doi\n domain_of:\n - Doi\n range: uriorcurie\n required: true\n pattern: ^doi:10.\\d{2,9}/.*$\n doi_provider:\n name: doi_provider\n description: The authority, or organization, the DOI is associated with.\n examples:\n - value: ess_dive\n description: The corresponding DOI is associated with ESS-DIVE.\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - NCIT:C74932\n rank: 1000\n alias: doi_provider\n owner: Doi\n domain_of:\n - Doi\n range: DoiProviderEnum\n doi_category:\n name: doi_category\n description: The resource type the corresponding doi resolves to.\n examples:\n - value: dataset_doi\n description: The corresponding DOI is a dataset resource type.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: doi_category\n owner: Doi\n domain_of:\n - Doi\n range: DoiCategoryEnum\n required: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Doi\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Doi\nrules:\n- preconditions:\n slot_conditions:\n doi_category:\n name: doi_category\n any_of:\n - equals_string: dataset_doi\n - equals_string: award_doi\n postconditions:\n slot_conditions:\n doi_provider:\n name: doi_provider\n required: true\n description: If doi_category is a publication_doi, then doi_provider is not required.\n Otherwise, doi_provider is required.\n title: dataset_award_dois_required\n\nURI: DoiCategoryEnum
"},{"location":"DoiCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description award_doi None A type of DOI that resolves to a funding authority dataset_doi None A type of DOI that resolves to generated data publication_doi None A type of DOI that resolves to a publication data_management_plan_doi None A type of DOI that resolves to a data management plan"},{"location":"DoiCategoryEnum/#slots","title":"Slots","text":"Name Description doi_category The resource type the corresponding doi resolves to"},{"location":"DoiCategoryEnum/#comments","title":"Comments","text":"name: DoiCategoryEnum\ncomments:\n- See especially the resourceTypeGeneral section of the DataCite PDF, on pp48-53 as\n of 2023-07-19\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://schema.datacite.org/meta/kernel-4.4/doc/DataCite-MetadataKernel_v4.4.pdf\n- https://api.crossref.org/types\nrank: 1000\npermissible_values:\n award_doi:\n text: award_doi\n description: A type of DOI that resolves to a funding authority.\n dataset_doi:\n text: dataset_doi\n description: A type of DOI that resolves to generated data.\n publication_doi:\n text: publication_doi\n description: A type of DOI that resolves to a publication.\n data_management_plan_doi:\n text: data_management_plan_doi\n description: A type of DOI that resolves to a data management plan.\n\nURI: DoiProviderEnum
"},{"location":"DoiProviderEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description emsl https://ror.org/04rc0xn13 jgi https://ror.org/04xm1d337 kbase https://ror.org/01znn6x10 osti https://ror.org/031478740 ess_dive https://ror.org/01t14bp54 massive None gsc None zenodo None edi https://ror.org/0330j0z60 figshare https://ror.org/041mxqs23"},{"location":"DoiProviderEnum/#slots","title":"Slots","text":"Name Description doi_provider The authority, or organization, the DOI is associated with"},{"location":"DoiProviderEnum/#see-also","title":"See Also","text":"name: DoiProviderEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:DoiProviderEnum\n- nmdc:ProcessingInstitutionEnum\n- nmdc:ExecutionResourceEnum\nrank: 1000\npermissible_values:\n emsl:\n text: emsl\n meaning: https://ror.org/04rc0xn13\n title: EMSL\n aliases:\n - Environmental Molecular Sciences Laboratory\n - EMSL\n jgi:\n text: jgi\n meaning: https://ror.org/04xm1d337\n title: JGI\n aliases:\n - Joint Genome Institute\n - JGI\n kbase:\n text: kbase\n meaning: https://ror.org/01znn6x10\n title: KBase\n aliases:\n - KBase\n osti:\n text: osti\n meaning: https://ror.org/031478740\n title: OSTI\n aliases:\n - Office of Scientific and Technical Information\n - OSTI\n ess_dive:\n text: ess_dive\n meaning: https://ror.org/01t14bp54\n title: ESS-DIVE\n aliases:\n - ESS-DIVE\n - Environmental System Science Data Infrastructure for a Virtual Ecosystem\n massive:\n text: massive\n title: MassIVE\n aliases:\n - MassIVE\n - Mass Spectrometry Virtual Environment\n gsc:\n text: gsc\n title: GSC\n aliases:\n - GSC\n - Genomic Standards Consortium\n zenodo:\n text: zenodo\n title: Zenodo\n aliases:\n - Zenodo\n edi:\n text: edi\n meaning: https://ror.org/0330j0z60\n title: EDI\n aliases:\n - EDI\n - Environmental Data Initiative\n figshare:\n text: figshare\n meaning: https://ror.org/041mxqs23\n title: Figshare\n\nURI: DoorCompTypeEnum
"},{"location":"DoorCompTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metal covered None revolving None sliding None telescopic None"},{"location":"DoorCompTypeEnum/#slots","title":"Slots","text":"Name Description door_comp_type The composite type of the door"},{"location":"DoorCompTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCompTypeEnum/#schema-source","title":"Schema Source","text":"name: door_comp_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metal covered:\n text: metal covered\n revolving:\n text: revolving\n sliding:\n text: sliding\n telescopic:\n text: telescopic\n\nURI: DoorCondEnum
"},{"location":"DoorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"DoorCondEnum/#slots","title":"Slots","text":"Name Description door_cond The phsical condition of the door"},{"location":"DoorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorCondEnum/#schema-source","title":"Schema Source","text":"name: door_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: DoorDirectEnum
"},{"location":"DoorDirectEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description inward None outward None sideways None"},{"location":"DoorDirectEnum/#slots","title":"Slots","text":"Name Description door_direct The direction the door opens"},{"location":"DoorDirectEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorDirectEnum/#schema-source","title":"Schema Source","text":"name: door_direct_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n inward:\n text: inward\n outward:\n text: outward\n sideways:\n text: sideways\n\nURI: DoorLocEnum
"},{"location":"DoorLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"DoorLocEnum/#slots","title":"Slots","text":"Name Description door_loc The relative location of the door in the room"},{"location":"DoorLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorLocEnum/#schema-source","title":"Schema Source","text":"name: door_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: DoorMatEnum
"},{"location":"DoorMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aluminum None cellular PVC None engineered plastic None fiberboard None fiberglass None metal None thermoplastic alloy None vinyl None wood None wood/plastic composite None"},{"location":"DoorMatEnum/#slots","title":"Slots","text":"Name Description door_mat The material the door is composed of"},{"location":"DoorMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMatEnum/#schema-source","title":"Schema Source","text":"name: door_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n aluminum:\n text: aluminum\n cellular PVC:\n text: cellular PVC\n engineered plastic:\n text: engineered plastic\n fiberboard:\n text: fiberboard\n fiberglass:\n text: fiberglass\n metal:\n text: metal\n thermoplastic alloy:\n text: thermoplastic alloy\n vinyl:\n text: vinyl\n wood:\n text: wood\n wood/plastic composite:\n text: wood/plastic composite\n\nURI: DoorMoveEnum
"},{"location":"DoorMoveEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None folding None revolving None rolling shutter None sliding None swinging None"},{"location":"DoorMoveEnum/#slots","title":"Slots","text":"Name Description door_move The type of movement of the door"},{"location":"DoorMoveEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorMoveEnum/#schema-source","title":"Schema Source","text":"name: door_move_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n collapsible:\n text: collapsible\n folding:\n text: folding\n revolving:\n text: revolving\n rolling shutter:\n text: rolling shutter\n sliding:\n text: sliding\n swinging:\n text: swinging\n\nURI: DoorTypeEnum
"},{"location":"DoorTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description composite None metal None wooden None"},{"location":"DoorTypeEnum/#slots","title":"Slots","text":"Name Description door_type The type of door material"},{"location":"DoorTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeEnum/#schema-source","title":"Schema Source","text":"name: door_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n composite:\n text: composite\n metal:\n text: metal\n wooden:\n text: wooden\n\nURI: DoorTypeMetalEnum
"},{"location":"DoorTypeMetalEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description collapsible None corrugated steel None hollow None rolling shutters None steel plate None"},{"location":"DoorTypeMetalEnum/#slots","title":"Slots","text":"Name Description door_type_metal The type of metal door"},{"location":"DoorTypeMetalEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeMetalEnum/#schema-source","title":"Schema Source","text":"name: door_type_metal_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n collapsible:\n text: collapsible\n corrugated steel:\n text: corrugated steel\n hollow:\n text: hollow\n rolling shutters:\n text: rolling shutters\n steel plate:\n text: steel plate\n\nURI: DoorTypeWoodEnum
"},{"location":"DoorTypeWoodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bettened and ledged None battened None ledged and braced None ledged and framed None ledged, braced and frame None framed and paneled None glashed or sash None flush None louvered None wire gauged None"},{"location":"DoorTypeWoodEnum/#slots","title":"Slots","text":"Name Description door_type_wood The type of wood door"},{"location":"DoorTypeWoodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DoorTypeWoodEnum/#schema-source","title":"Schema Source","text":"name: door_type_wood_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bettened and ledged:\n text: bettened and ledged\n battened:\n text: battened\n ledged and braced:\n text: ledged and braced\n ledged and framed:\n text: ledged and framed\n ledged, braced and frame:\n text: ledged, braced and frame\n framed and paneled:\n text: framed and paneled\n glashed or sash:\n text: glashed or sash\n flush:\n text: flush\n louvered:\n text: louvered\n wire gauged:\n text: wire gauged\n\nA real number that conforms to the xsd:double specification
URI: xsd:double
base: float
uri: xsd:double
URI: DrainageClassEnum
"},{"location":"DrainageClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description very poorly None poorly None somewhat poorly None moderately well None well None excessively drained None"},{"location":"DrainageClassEnum/#slots","title":"Slots","text":"Name Description drainage_class Drainage classification from a standard system such as the USDA system"},{"location":"DrainageClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrainageClassEnum/#schema-source","title":"Schema Source","text":"name: drainage_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n very poorly:\n text: very poorly\n poorly:\n text: poorly\n somewhat poorly:\n text: somewhat poorly\n moderately well:\n text: moderately well\n well:\n text: well\n excessively drained:\n text: excessively drained\n\nURI: DrawingsEnum
"},{"location":"DrawingsEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None building navigation map None diagram None sketch None"},{"location":"DrawingsEnum/#slots","title":"Slots","text":"Name Description drawings The buildings architectural drawings; if design is chosen, indicate phase-con..."},{"location":"DrawingsEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"DrawingsEnum/#schema-source","title":"Schema Source","text":"name: drawings_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n operation:\n text: operation\n as built:\n text: as built\n construction:\n text: construction\n bid:\n text: bid\n design:\n text: design\n building navigation map:\n text: building navigation map\n diagram:\n text: diagram\n sketch:\n text: sketch\n\nURI: EluentIntroductionCategoryEnum
"},{"location":"EluentIntroductionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description liquid_chromatography None The processed sample is introduced into the mass spectrometer through a liqui... gas_chromatography None The processed sample is introduced into the mass spectrometer through a gas c... direct_infusion_syringe None The processed sample is introduced into the mass spectrometer through a direc... direct_infusion_autosampler None The processed sample is introduced into the mass spectrometer through a direc..."},{"location":"EluentIntroductionCategoryEnum/#slots","title":"Slots","text":"Name Description eluent_introduction_category A high-level categorization for how the processed sample is introduced into a..."},{"location":"EluentIntroductionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"EluentIntroductionCategoryEnum/#schema-source","title":"Schema Source","text":"name: EluentIntroductionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n liquid_chromatography:\n text: liquid_chromatography\n description: The processed sample is introduced into the mass spectrometer through\n a liquid chromatography process.\n aliases:\n - LC\n gas_chromatography:\n text: gas_chromatography\n description: The processed sample is introduced into the mass spectrometer through\n a gas chromatography process.\n aliases:\n - GC\n direct_infusion_syringe:\n text: direct_infusion_syringe\n description: The processed sample is introduced into the mass spectrometer through\n a direct infusion process using a syringe.\n direct_infusion_autosampler:\n text: direct_infusion_autosampler\n description: The processed sample is introduced into the mass spectrometer through\n a direct infusion process using an autosampler.\n\nURI: nmdc:EnvironmentalMaterialTerm
classDiagram\n class EnvironmentalMaterialTerm\n click EnvironmentalMaterialTerm href \"../EnvironmentalMaterialTerm\"\n OntologyClass <|-- EnvironmentalMaterialTerm\n click OntologyClass href \"../OntologyClass\"\n\n\n\n EnvironmentalMaterialTerm : alternative_identifiers\n\n EnvironmentalMaterialTerm : alternative_names\n\n EnvironmentalMaterialTerm : definition\n\n EnvironmentalMaterialTerm : description\n\n EnvironmentalMaterialTerm : id\n\n EnvironmentalMaterialTerm : name\n\n EnvironmentalMaterialTerm : relations\n\n EnvironmentalMaterialTerm --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n EnvironmentalMaterialTerm : type\n\n\n\nname: EnvironmentalMaterialTerm\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nclass_uri: nmdc:EnvironmentalMaterialTerm\n\nname: EnvironmentalMaterialTerm\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: OntologyClass\nattributes:\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: EnvironmentalMaterialTerm\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: EnvironmentalMaterialTerm\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: EnvironmentalMaterialTerm\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: EnvironmentalMaterialTerm\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: EnvironmentalMaterialTerm\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: EnvironmentalMaterialTerm\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: EnvironmentalMaterialTerm\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: EnvironmentalMaterialTerm\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:EnvironmentalMaterialTerm\n\nThis class contains information pertaining to evaluating if a Metagenome-Assembled Genome (MAG) is eukaryotic.
URI: nmdc:EukEval
classDiagram\n class EukEval\n click EukEval href \"../EukEval\"\n\n EukEval : completeness\n\n EukEval : contamination\n\n EukEval : ncbi_lineage\n\n EukEval : ncbi_lineage_tax_ids\n\n EukEval : type\n\n\n\nname: EukEval\ndescription: This class contains information pertaining to evaluating if a Metagenome-Assembled\n Genome (MAG) is eukaryotic.\ncomments:\n- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information\n for this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- type\n- completeness\n- contamination\n- ncbi_lineage_tax_ids\n- ncbi_lineage\nclass_uri: nmdc:EukEval\n\nname: EukEval\ndescription: This class contains information pertaining to evaluating if a Metagenome-Assembled\n Genome (MAG) is eukaryotic.\ncomments:\n- A tool like eukCC (https://doi.org/10.1186/s13059-020-02155-4) would generate information\n for this class.\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: EukEval\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n completeness:\n name: completeness\n description: Estimate of the completeness of the metagenome-assembled genome,\n estimated by a tool like CheckM.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: completeness\n owner: EukEval\n domain_of:\n - EukEval\n - MagBin\n range: float\n minimum_value: 0\n contamination:\n name: contamination\n description: Estimate of the completeness of the metagenome-assembled genome,\n estimated by a tool like CheckM.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contamination\n owner: EukEval\n domain_of:\n - EukEval\n - MagBin\n range: float\n minimum_value: 0\n ncbi_lineage_tax_ids:\n name: ncbi_lineage_tax_ids\n description: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)\n comments:\n - Example 1-131567-2759-2611352-33682-191814-2603949\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_lineage_tax_ids\n owner: EukEval\n domain_of:\n - EukEval\n range: string\n pattern: ^\\d+(-\\d+)*$\n ncbi_lineage:\n name: ncbi_lineage\n description: Comma delimited ordered list of NCBI taxonomy names.\n comments:\n - Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_lineage\n owner: EukEval\n domain_of:\n - EukEval\n range: string\nclass_uri: nmdc:EukEval\n\nURI: ExecutionResourceEnum
"},{"location":"ExecutionResourceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description NERSC-Cori None NERSC Cori supercomputer NERSC-Perlmutter None NERSC Perlmutter supercomputer EMSL None Environmental Molecular Sciences Laboratory EMSL-RZR None Environmental Molecular Sciences Laboratory RZR cluster JGI None Joint Genome Institute LANL-B-div None LANL Bioscience Division"},{"location":"ExecutionResourceEnum/#slots","title":"Slots","text":"Name Description execution_resource The computing resource or facility where the workflow was executed"},{"location":"ExecutionResourceEnum/#see-also","title":"See Also","text":"name: ExecutionResourceEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:DoiProviderEnum\n- nmdc:ProcessingInstitutionEnum\n- nmdc:ExecutionResourceEnum\nrank: 1000\npermissible_values:\n NERSC-Cori:\n text: NERSC-Cori\n description: NERSC Cori supercomputer\n aliases:\n - Cori\n NERSC-Perlmutter:\n text: NERSC-Perlmutter\n description: NERSC Perlmutter supercomputer\n aliases:\n - Perlmutter\n - Saul\n EMSL:\n text: EMSL\n description: Environmental Molecular Sciences Laboratory\n EMSL-RZR:\n text: EMSL-RZR\n description: Environmental Molecular Sciences Laboratory RZR cluster\n aliases:\n - RZR\n JGI:\n text: JGI\n description: Joint Genome Institute\n LANL-B-div:\n text: LANL-B-div\n description: LANL Bioscience Division\n aliases:\n - B-div\n\nURI: ExtWallOrientEnum
"},{"location":"ExtWallOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWallOrientEnum/#slots","title":"Slots","text":"Name Description ext_wall_orient The orientation of the exterior wall"},{"location":"ExtWallOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWallOrientEnum/#schema-source","title":"Schema Source","text":"name: ext_wall_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n northeast:\n text: northeast\n southeast:\n text: southeast\n southwest:\n text: southwest\n northwest:\n text: northwest\n\nURI: ExtWindowOrientEnum
"},{"location":"ExtWindowOrientEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None northeast None southeast None southwest None northwest None"},{"location":"ExtWindowOrientEnum/#slots","title":"Slots","text":"Name Description ext_window_orient The compass direction the exterior window of the room is facing"},{"location":"ExtWindowOrientEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtWindowOrientEnum/#schema-source","title":"Schema Source","text":"name: ext_window_orient_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n northeast:\n text: northeast\n southeast:\n text: southeast\n southwest:\n text: southwest\n northwest:\n text: northwest\n\nA CURIE representing an external identifier
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
typeof: uriorcurie
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
A material separation in which a desired component of an input material is separated from the remainder.
URI: nmdc:Extraction
classDiagram\n class Extraction\n click Extraction href \"../Extraction\"\n MaterialProcessing <|-- Extraction\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n Extraction : alternative_identifiers\n\n Extraction : description\n\n Extraction : end_date\n\n Extraction : extraction_targets\n\n Extraction --> \"*\" ExtractionTargetEnum : extraction_targets\n click ExtractionTargetEnum href \"../ExtractionTargetEnum\"\n\n Extraction : has_failure_categorization\n\n Extraction --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n Extraction : has_input\n\n Extraction --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n Extraction : has_output\n\n Extraction --> \"1..*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n Extraction : id\n\n Extraction : input_mass\n\n Extraction --> \"0..1\" QuantityValue : input_mass\n click QuantityValue href \"../QuantityValue\"\n\n Extraction : instrument_used\n\n Extraction --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n Extraction : name\n\n Extraction : processing_institution\n\n Extraction --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n Extraction : protocol_link\n\n Extraction --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n Extraction : qc_comment\n\n Extraction : qc_status\n\n Extraction --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n Extraction : start_date\n\n Extraction : substances_used\n\n Extraction --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n Extraction : type\n\n Extraction : volume\n\n Extraction --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: Extraction\ndescription: A material separation in which a desired component of an input material\n is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: MaterialProcessing\nslots:\n- substances_used\n- extraction_targets\n- input_mass\n- volume\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The volume of the solvent/solute being used, not the input.\nclass_uri: nmdc:Extraction\n\nname: Extraction\ndescription: A material separation in which a desired component of an input material\n is separated from the remainder.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0302884\nis_a: MaterialProcessing\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The volume of the solvent/solute being used, not the input.\nattributes:\n substances_used:\n name: substances_used\n description: The substances that are combined to enable a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: Extraction\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n extraction_targets:\n name: extraction_targets\n description: Provides the target biomolecule that has been separated from a sample\n during an extraction process.\n notes:\n - todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)\n from_schema: https://w3id.org/nmdc/nmdc\n narrow_mappings:\n - NCIT:C177560\n - MIXS:0000037\n rank: 1000\n alias: extraction_targets\n owner: Extraction\n domain_of:\n - Extraction\n range: ExtractionTargetEnum\n multivalued: true\n input_mass:\n name: input_mass\n description: Total mass of sample used in activity.\n title: sample mass used\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - sample mass\n - sample weight\n exact_mappings:\n - MS:1000004\n narrow_mappings:\n - MIXS:0000111\n rank: 1000\n alias: input_mass\n owner: Extraction\n domain_of:\n - Extraction\n range: QuantityValue\n volume:\n name: volume\n description: The volume of the solvent/solute being used, not the input.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: Extraction\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: Extraction\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Extraction\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: Extraction\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Extraction\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Extraction\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Extraction\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Extraction\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Extraction\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Extraction\n\nURI: ExtractionTargetEnum
"},{"location":"ExtractionTargetEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None metabolite None protein None lipid None"},{"location":"ExtractionTargetEnum/#slots","title":"Slots","text":"Name Description extraction_targets Provides the target biomolecule that has been separated from a sample during ..."},{"location":"ExtractionTargetEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ExtractionTargetEnum/#schema-source","title":"Schema Source","text":"name: ExtractionTargetEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DNA:\n text: DNA\n RNA:\n text: RNA\n metabolite:\n text: metabolite\n protein:\n text: protein\n lipid:\n text: lipid\n\nURI: nmdc:FailureCategorization
classDiagram\n class FailureCategorization\n click FailureCategorization href \"../FailureCategorization\"\n\n FailureCategorization : qc_failure_what\n\n FailureCategorization --> \"0..1\" FailureWhatEnum : qc_failure_what\n click FailureWhatEnum href \"../FailureWhatEnum\"\n\n FailureCategorization : qc_failure_where\n\n FailureCategorization --> \"0..1\" FailureWhereEnum : qc_failure_where\n click FailureWhereEnum href \"../FailureWhereEnum\"\n\n FailureCategorization : type\n\n\n\nname: FailureCategorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- qc_failure_what\n- qc_failure_where\n- type\nclass_uri: nmdc:FailureCategorization\n\nname: FailureCategorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n qc_failure_what:\n name: qc_failure_what\n description: Provides a summary about what caused a lab or workflow process to\n fail\n comments:\n - For example, low read count from a sequencer, malformed fastq files, etc.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_failure_what\n owner: FailureCategorization\n domain_of:\n - FailureCategorization\n range: FailureWhatEnum\n qc_failure_where:\n name: qc_failure_where\n description: Describes the nmdc schema class that corresonds to where the failure\n occurred. Most commonly this would be the same as Class that generated the results.\n comments:\n - If the assembly size was too small to proceed to annotation failure_where would\n be MetagenomeAssembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_failure_where\n owner: FailureCategorization\n domain_of:\n - FailureCategorization\n range: FailureWhereEnum\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FailureCategorization\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FailureCategorization\n\nThe permitted values for describing where a failure occurred during processing in the lab during analysis workflows.
URI: FailureWhatEnum
"},{"location":"FailureWhatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low_read_count None Number of output reads is not sufficient to continue to the next analysis ste... malformed_data None Workflow failure reading input or writing the output file(s) assembly_size_too_small None The size of the metagenome or metatranscriptome assembly is too small to proc... no_valid_data_generated None A process ran but did not produce any output other None A lab process or analysis workflow has failed in a way that has not been capt..."},{"location":"FailureWhatEnum/#slots","title":"Slots","text":"Name Description qc_failure_what Provides a summary about what caused a lab or workflow process to fail"},{"location":"FailureWhatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FailureWhatEnum/#schema-source","title":"Schema Source","text":"name: FailureWhatEnum\ndescription: The permitted values for describing where a failure occurred during processing\n in the lab during analysis workflows.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n low_read_count:\n text: low_read_count\n description: Number of output reads is not sufficient to continue to the next\n analysis step.\n malformed_data:\n text: malformed_data\n description: Workflow failure reading input or writing the output file(s).\n assembly_size_too_small:\n text: assembly_size_too_small\n description: The size of the metagenome or metatranscriptome assembly is too small\n to proceed to the next analysis workflow.\n no_valid_data_generated:\n text: no_valid_data_generated\n description: A process ran but did not produce any output. Ie binning ran but\n did not produce any medium or high quality bins.\n other:\n text: other\n description: A lab process or analysis workflow has failed in a way that has not\n been captured by the available values yet. Please use slot 'qc_comment' to specify\n details.\n\nThe permitted values for describing where in the process, either a lab or analysis workflow step, the failure occurred.
URI: FailureWhereEnum
"},{"location":"FailureWhereEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description NucleotideSequencing None A failure has occurred during nucleotide sequencing, a data generation proces... MassSpectrometry None A failure has occurred during mass spectrometry, a data generation process Pooling None A failure has occurred in pooling, a lab process Extraction None A failure has occurred in extraction, a lab process LibraryPreparation None A failure has occurred in library preparation, a lab process MetagenomeAssembly None A failure has occurred in metagenome assembly, a workflow process MetatranscriptomeExpressionAnalysis None A failure has occurred in metatranscriptome expression analysis, a workflow p... MagsAnalysis None A failure has occurred in binning, a workflow process to generate metagenome-... ReadQcAnalysis None A failure has occurred in read qc, a workflow process ReadBasedTaxonomyAnalysis None A failure has occurred in reads based taxonomy, a workflow process MetagenomeAnnotation None A failure has occurred in annotation, a workflow process MetatranscriptomeAssembly None A failure has occurred in assembly, a workflow process MetatranscriptomeAnnotation None A failure has occurred in annotation, a workflow process MetabolomicsAnalysis None A failure has occurred in analyzing metabolomics data MetaproteomicsAnalysis None A failure has occurred in analyzing metaproteomics data NomAnalysis None A failure has occurred in analyzing NOM data"},{"location":"FailureWhereEnum/#slots","title":"Slots","text":"Name Description qc_failure_where Describes the nmdc schema class that corresonds to where the failure occurred"},{"location":"FailureWhereEnum/#comments","title":"Comments","text":"name: FailureWhereEnum\ndescription: The permitted values for describing where in the process, either a lab\n or analysis workflow step, the failure occurred.\ncomments:\n- At Chris' recommendation permissible values for this enumeration are the same as\n Class names.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n NucleotideSequencing:\n text: NucleotideSequencing\n description: A failure has occurred during nucleotide sequencing, a data generation\n process.\n MassSpectrometry:\n text: MassSpectrometry\n description: A failure has occurred during mass spectrometry, a data generation\n process.\n Pooling:\n text: Pooling\n description: A failure has occurred in pooling, a lab process.\n Extraction:\n text: Extraction\n description: A failure has occurred in extraction, a lab process.\n LibraryPreparation:\n text: LibraryPreparation\n description: A failure has occurred in library preparation, a lab process.\n MetagenomeAssembly:\n text: MetagenomeAssembly\n description: A failure has occurred in metagenome assembly, a workflow process.\n MetatranscriptomeExpressionAnalysis:\n text: MetatranscriptomeExpressionAnalysis\n description: A failure has occurred in metatranscriptome expression analysis,\n a workflow process.\n MagsAnalysis:\n text: MagsAnalysis\n description: A failure has occurred in binning, a workflow process to generate\n metagenome-assembled genomes (MAGS).\n ReadQcAnalysis:\n text: ReadQcAnalysis\n description: A failure has occurred in read qc, a workflow process.\n ReadBasedTaxonomyAnalysis:\n text: ReadBasedTaxonomyAnalysis\n description: A failure has occurred in reads based taxonomy, a workflow process.\n MetagenomeAnnotation:\n text: MetagenomeAnnotation\n description: A failure has occurred in annotation, a workflow process.\n MetatranscriptomeAssembly:\n text: MetatranscriptomeAssembly\n description: A failure has occurred in assembly, a workflow process.\n MetatranscriptomeAnnotation:\n text: MetatranscriptomeAnnotation\n description: A failure has occurred in annotation, a workflow process.\n MetabolomicsAnalysis:\n text: MetabolomicsAnalysis\n description: A failure has occurred in analyzing metabolomics data.\n MetaproteomicsAnalysis:\n text: MetaproteomicsAnalysis\n description: A failure has occurred in analyzing metaproteomics data.\n NomAnalysis:\n text: NomAnalysis\n description: A failure has occurred in analyzing NOM data.\n\nURI: FaoClassEnum
"},{"location":"FaoClassEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Acrisols None Andosols None Arenosols None Cambisols None Chernozems None Ferralsols None Fluvisols None Gleysols None Greyzems None Gypsisols None Histosols None Kastanozems None Lithosols None Luvisols None Nitosols None Phaeozems None Planosols None Podzols None Podzoluvisols None Rankers None Regosols None Rendzinas None Solonchaks None Solonetz None Vertisols None Yermosols None"},{"location":"FaoClassEnum/#slots","title":"Slots","text":"Name Description fao_class Soil classification from the FAO World Reference Database for Soil Resources"},{"location":"FaoClassEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FaoClassEnum/#schema-source","title":"Schema Source","text":"name: fao_class_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Acrisols:\n text: Acrisols\n Andosols:\n text: Andosols\n Arenosols:\n text: Arenosols\n Cambisols:\n text: Cambisols\n Chernozems:\n text: Chernozems\n Ferralsols:\n text: Ferralsols\n Fluvisols:\n text: Fluvisols\n Gleysols:\n text: Gleysols\n Greyzems:\n text: Greyzems\n Gypsisols:\n text: Gypsisols\n Histosols:\n text: Histosols\n Kastanozems:\n text: Kastanozems\n Lithosols:\n text: Lithosols\n Luvisols:\n text: Luvisols\n Nitosols:\n text: Nitosols\n Phaeozems:\n text: Phaeozems\n Planosols:\n text: Planosols\n Podzols:\n text: Podzols\n Podzoluvisols:\n text: Podzoluvisols\n Rankers:\n text: Rankers\n Regosols:\n text: Regosols\n Rendzinas:\n text: Rendzinas\n Solonchaks:\n text: Solonchaks\n Solonetz:\n text: Solonetz\n Vertisols:\n text: Vertisols\n Yermosols:\n text: Yermosols\n\nA site, outside of a laboratory, from which biosamples may be collected.
URI: nmdc:FieldResearchSite
classDiagram\n class FieldResearchSite\n click FieldResearchSite href \"../FieldResearchSite\"\n Site <|-- FieldResearchSite\n click Site href \"../Site\"\n\n\n\n FieldResearchSite : alternative_identifiers\n\n FieldResearchSite : cur_vegetation\n\n FieldResearchSite --> \"0..1\" TextValue : cur_vegetation\n click TextValue href \"../TextValue\"\n\n FieldResearchSite : description\n\n FieldResearchSite : elev\n\n FieldResearchSite : geo_loc_name\n\n FieldResearchSite --> \"0..1\" TextValue : geo_loc_name\n click TextValue href \"../TextValue\"\n\n FieldResearchSite : habitat\n\n FieldResearchSite : id\n\n FieldResearchSite : lat_lon\n\n FieldResearchSite --> \"0..1\" GeolocationValue : lat_lon\n click GeolocationValue href \"../GeolocationValue\"\n\n FieldResearchSite : local_class\n\n FieldResearchSite --> \"0..1\" TextValue : local_class\n click TextValue href \"../TextValue\"\n\n FieldResearchSite : name\n\n FieldResearchSite : part_of\n\n FieldResearchSite --> \"*\" FieldResearchSite : part_of\n click FieldResearchSite href \"../FieldResearchSite\"\n\n FieldResearchSite : soil_type\n\n FieldResearchSite --> \"0..1\" TextValue : soil_type\n click TextValue href \"../TextValue\"\n\n FieldResearchSite : type\n\n\n\nname: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n same plant were obtained at the same site. In this case, the site would correspond\n to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslots:\n- cur_vegetation\n- elev\n- geo_loc_name\n- habitat\n- lat_lon\n- local_class\n- part_of\n- soil_type\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n part_of:\n name: part_of\n range: FieldResearchSite\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:FieldResearchSite\n\nname: FieldResearchSite\ndescription: A site, outside of a laboratory, from which biosamples may be collected.\ntitle: Field Research Site\ncomments:\n- Provides grouping of biosamples at level that's more specific than belonging to\n the same study\n- be very clear that this could be part of a larger site\n- In Bioscales, one might say that rhizosphere soil and bulk soil from around the\n same plant were obtained at the same site. In this case, the site would correspond\n to one tree.\n- might correspond to GOLD's identifier on a page like https://gold.jgi.doe.gov/biosample?id=Gb0305833\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- research plot\nis_a: Site\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n part_of:\n name: part_of\n range: FieldResearchSite\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n cur_vegetation:\n name: cur_vegetation\n annotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\n description: Vegetation classification from one or more standard classification\n systems, or agricultural crop\n title: current vegetation\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - current vegetation\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000312\n alias: cur_vegetation\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n elev:\n name: elev\n annotations:\n expected_value:\n tag: expected_value\n value: measurement value\n description: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the\n surface, such as an aircraft in flight or a spacecraft in orbit.\n title: elevation\n examples:\n - value: 100 meter\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - elevation\n rank: 1000\n is_a: environment field\n slot_uri: MIXS:0000093\n alias: elev\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: float\n multivalued: false\n geo_loc_name:\n name: geo_loc_name\n annotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location\n name'\n description: The geographical origin of the sample as defined by the country or\n sea name followed by specific region name. Country or sea names should be chosen\n from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology\n (http://purl.bioontology.org/ontology/GAZ)\n title: geographic location (country and/or sea,region)\n examples:\n - value: 'USA: Maryland, Bethesda'\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (country and/or sea,region)\n rank: 1000\n is_a: environment field\n string_serialization: '{term}: {term}, {text}'\n slot_uri: MIXS:0000010\n alias: geo_loc_name\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n habitat:\n name: habitat\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: habitat\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: string\n lat_lon:\n name: lat_lon\n annotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\n description: The geographical origin of the sample as defined by latitude and\n longitude. The values should be reported in decimal degrees and in WGS84 system\n title: geographic location (latitude and longitude)\n examples:\n - value: 50.586825 6.408977\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - geographic location (latitude and longitude)\n rank: 1000\n is_a: environment field\n string_serialization: '{float} {float}'\n slot_uri: MIXS:0000009\n alias: lat_lon\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: GeolocationValue\n multivalued: false\n local_class:\n name: local_class\n annotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\n description: Soil classification based on local soil classification system\n title: soil_taxonomic/local classification\n examples:\n - value: ''\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil_taxonomic/local classification\n rank: 1000\n is_a: core field\n string_serialization: '{text}'\n slot_uri: MIXS:0000330\n alias: local_class\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n part_of:\n name: part_of\n description: Links a resource to another resource that either logically or physically\n includes it.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n slot_uri: dcterms:isPartOf\n alias: part_of\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Study\n range: FieldResearchSite\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n soil_type:\n name: soil_type\n annotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\n description: Description of the soil type or classification. This field accepts\n terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms\n can be separated by pipes.\n title: soil type\n examples:\n - value: plinthosol [ENVO:00002250]\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - soil type\n rank: 1000\n is_a: core field\n string_serialization: '{termLabel} {[termID]}'\n slot_uri: MIXS:0000332\n alias: soil_type\n owner: FieldResearchSite\n domain_of:\n - FieldResearchSite\n - Biosample\n range: TextValue\n multivalued: false\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: FieldResearchSite\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:frsite-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FieldResearchSite\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FieldResearchSite\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: FieldResearchSite\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FieldResearchSite\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FieldResearchSite\n\nURI: FileTypeEnum
"},{"location":"FileTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Virus Summary None Tab separated file listing the viruses found by geNomad Plasmid Summary None Tab separated file listing the plasmids found be geNomad GeNomad Aggregated Classification None Tab separated file which combines the results from neural network-based class... Reference Calibration File None A file that contains data used to calibrate a natural organic matter or metab... Metagenome Raw Reads None Interleaved paired-end raw sequencing data Metagenome Raw Read 1 None Read 1 raw sequencing data, aka forward reads Metagenome Raw Read 2 None Read 2 raw sequencing data, aka reverse reads FT ICR-MS Analysis Results None FT ICR-MS-based molecular formula assignment results table GC-MS Metabolomics Results None GC-MS-based metabolite assignment results table Metaproteomics Workflow Statistics None Aggregate workflow statistics file Protein Report None Filtered protein report file Peptide Report None Filtered peptide report file Unfiltered Metaproteomics Results None MSGFjobs and MASIC output file Read Count and RPKM None Annotation read count and RPKM per feature JSON QC non-rRNA R2 None QC removed rRNA reads (R2) fastq QC non-rRNA R1 None QC removed rRNA reads (R1) fastq Metagenome Bins None Metagenome bin contigs fasta Metagenome HQMQ Bins Compression File None Compressed file containing high qulaity and medium quality metagenome bins an... Metagenome LQ Bins Compression File None Compressed file containing low quality metagenome bins and associated files Metagenome Bins Info File None File containing version information on the binning workflow CheckM Statistics None CheckM statistics report Metagenome Bins Heatmap None The Heatmap presents the pdf file containing the KO analysis results for meta... Metagenome Bins Barplot None The Bar chart presents the pdf file containing the KO analysis results for me... Metagenome Bins Krona Plot None The Krona plot presents the HTML file containing the KO analysis results for ... Read Based Analysis Info File None File containing reads based analysis information GTDBTK Bacterial Summary None GTDBTK bacterial summary GTDBTK Archaeal Summary None GTDBTK archaeal summary GOTTCHA2 Krona Plot None GOTTCHA2 krona plot HTML file GOTTCHA2 Classification Report None GOTTCHA2 classification report file GOTTCHA2 Report Full None GOTTCHA2 report file Kraken2 Krona Plot None Kraken2 krona plot HTML file Centrifuge Krona Plot None Centrifuge krona plot HTML file Centrifuge output report file None Centrifuge output report file Kraken2 Classification Report None Kraken2 output report file Kraken2 Taxonomic Classification None Kraken2 output read classification file Centrifuge Classification Report None Centrifuge output report file Centrifuge Taxonomic Classification None Centrifuge output read classification file Structural Annotation GFF None GFF3 format file with structural annotations Structural Annotation Stats Json None Structural annotations stats json Functional Annotation GFF None GFF3 format file with functional annotations Annotation Info File None File containing annotation info Annotation Amino Acid FASTA None FASTA amino acid file for annotated proteins Annotation Enzyme Commission None Tab delimited file for EC annotation Annotation KEGG Orthology None Tab delimited file for KO annotation Assembly Info File None File containing assembly info Assembly Coverage BAM None Sorted bam file of reads mapping back to the final assembly Assembly AGP None An AGP format file that describes the assembly Assembly Scaffolds None Final assembly scaffolds fasta Assembly Contigs None Final assembly contigs fasta Assembly Coverage Stats None Assembled contigs coverage information Contig Mapping File None Contig mappings between contigs and scaffolds Error Corrected Reads None Error corrected reads fastq Filtered Sequencing Reads None Reads QC result fastq (clean data) Read Filtering Info File None File containing read filtering information QC Statistics Extended None Extended report including methods and results for read filtering QC Statistics None Reads QC summary statistics TIGRFam Annotation GFF None GFF3 format file with TIGRfam CRT Annotation GFF None GFF3 format file with CRT Genemark Annotation GFF None GFF3 format file with Genemark Prodigal Annotation GFF None GFF3 format file with Prodigal TRNA Annotation GFF None GFF3 format file with TRNA Misc Annotation GFF None GFF3 format file with Misc RFAM Annotation GFF None GFF3 format file with RFAM TMRNA Annotation GFF None GFF3 format file with TMRNA Crispr Terms None Crispr Terms Product Names None Product names file Gene Phylogeny tsv None Gene Phylogeny tsv Scaffold Lineage tsv None phylogeny at the scaffold level Clusters of Orthologous Groups (COG) Annotation GFF None GFF3 format file with COGs KO_EC Annotation GFF None GFF3 format file with KO_EC CATH FunFams (Functional Families) Annotation GFF None GFF3 format file with CATH FunFams SUPERFam Annotation GFF None GFF3 format file with SUPERFam SMART Annotation GFF None GFF3 format file with SMART Pfam Annotation GFF None GFF3 format file with Pfam Annotation Statistics None Annotation statistics report Direct Infusion FT ICR-MS Raw Data None Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance mass spect... LC-DDA-MS/MS Raw Data None Liquid chromatographically separated MS1 and Data-Dependent MS2 binary instru... Configuration toml None A configuration toml file used by various programs to store settings that are... LC-MS Lipidomics Results None LC-MS-based lipidomics analysis results table LC-MS Lipidomics Processed Data None Processed data for the LC-MS-based lipidomics analysis in hdf5 format Contaminants Amino Acid FASTA None FASTA amino acid file for contaminant proteins commonly observed in proteomic... Analysis Tool Parameter File None A configuration file used by a single computational software tool that stores... Workflow Operation Summary None A human readable record of analysis steps applied during an instance of a wor... Metatranscriptome Expression None Metatranscriptome expression values and read counts for gene features predict... Metatranscriptome Expression Intergenic None Metatranscriptome expression values and read counts for intergenic regions Metatranscriptome Expression Info File None File containing version information on the expression workflow rRNA Filtered Sequencing Reads None File containing ribosomal reads from the read qc filtering step BAI File None An index file found in the same directory as the binary alignment map (BAM) f..."},{"location":"FileTypeEnum/#slots","title":"Slots","text":"Name Description data_object_type The type of file represented by the data object"},{"location":"FileTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FileTypeEnum/#schema-source","title":"Schema Source","text":"name: FileTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Virus Summary:\n text: Virus Summary\n description: Tab separated file listing the viruses found by geNomad.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^_virus_summary\\.tsv?$\n see_also:\n - https://portal.nersc.gov/genomad/\n Plasmid Summary:\n text: Plasmid Summary\n description: Tab separated file listing the plasmids found be geNomad.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^_plasmid_summary\\.tsv?$\n see_also:\n - https://portal.nersc.gov/genomad/\n GeNomad Aggregated Classification:\n text: GeNomad Aggregated Classification\n description: Tab separated file which combines the results from neural network-based\n classification and marker-based classification for virus and plasmid detection\n with geNomad.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^_aggregated_classification\\.tsv?$\n see_also:\n - https://portal.nersc.gov/genomad/\n Reference Calibration File:\n text: Reference Calibration File\n description: A file that contains data used to calibrate a natural organic matter\n or metabalomics analysis.\n Metagenome Raw Reads:\n text: Metagenome Raw Reads\n description: Interleaved paired-end raw sequencing data\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^\\.fastq(\\.gz)?$\n Metagenome Raw Read 1:\n text: Metagenome Raw Read 1\n description: Read 1 raw sequencing data, aka forward reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^.+_R1\\.fastq(\\.gz)?$\n examples:\n - value: BMI_H25VYBGXH_19S_31WellG1_R1.fastq.gz\n Metagenome Raw Read 2:\n text: Metagenome Raw Read 2\n description: Read 2 raw sequencing data, aka reverse reads\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: ^.+_R2\\.fastq(\\.gz)?$\n examples:\n - value: BMI_H25VYBGXH_19S_31WellG1_R2.fastq.gz\n FT ICR-MS Analysis Results:\n text: FT ICR-MS Analysis Results\n description: FT ICR-MS-based molecular formula assignment results table\n GC-MS Metabolomics Results:\n text: GC-MS Metabolomics Results\n description: GC-MS-based metabolite assignment results table\n Metaproteomics Workflow Statistics:\n text: Metaproteomics Workflow Statistics\n description: Aggregate workflow statistics file\n Protein Report:\n text: Protein Report\n description: Filtered protein report file\n Peptide Report:\n text: Peptide Report\n description: Filtered peptide report file\n Unfiltered Metaproteomics Results:\n text: Unfiltered Metaproteomics Results\n description: MSGFjobs and MASIC output file\n Read Count and RPKM:\n text: Read Count and RPKM\n description: Annotation read count and RPKM per feature JSON\n QC non-rRNA R2:\n text: QC non-rRNA R2\n description: QC removed rRNA reads (R2) fastq\n QC non-rRNA R1:\n text: QC non-rRNA R1\n description: QC removed rRNA reads (R1) fastq\n Metagenome Bins:\n text: Metagenome Bins\n description: Metagenome bin contigs fasta\n Metagenome HQMQ Bins Compression File:\n text: Metagenome HQMQ Bins Compression File\n description: Compressed file containing high qulaity and medium quality metagenome\n bins and associated files\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_hqmq_bin.zip'\n Metagenome LQ Bins Compression File:\n text: Metagenome LQ Bins Compression File\n description: Compressed file containing low quality metagenome bins and associated\n files\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_lq_bin.zip'\n Metagenome Bins Info File:\n text: Metagenome Bins Info File\n description: File containing version information on the binning workflow\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_bin.info'\n CheckM Statistics:\n text: CheckM Statistics\n description: CheckM statistics report\n Metagenome Bins Heatmap:\n text: Metagenome Bins Heatmap\n description: The Heatmap presents the pdf file containing the KO analysis results\n for metagenome bins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_heatmap.pdf'\n Metagenome Bins Barplot:\n text: Metagenome Bins Barplot\n description: The Bar chart presents the pdf file containing the KO analysis results\n for metagenome bins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_barplot.pdf'\n Metagenome Bins Krona Plot:\n text: Metagenome Bins Krona Plot\n description: The Krona plot presents the HTML file containing the KO analysis\n results for metagenome bins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[mag_wf_activity_id]_kronaplot.html'\n Read Based Analysis Info File:\n text: Read Based Analysis Info File\n description: File containing reads based analysis information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: profiler.info\n GTDBTK Bacterial Summary:\n text: GTDBTK Bacterial Summary\n description: GTDBTK bacterial summary\n GTDBTK Archaeal Summary:\n text: GTDBTK Archaeal Summary\n description: GTDBTK archaeal summary\n GOTTCHA2 Krona Plot:\n text: GOTTCHA2 Krona Plot\n description: GOTTCHA2 krona plot HTML file\n GOTTCHA2 Classification Report:\n text: GOTTCHA2 Classification Report\n description: GOTTCHA2 classification report file\n GOTTCHA2 Report Full:\n text: GOTTCHA2 Report Full\n description: GOTTCHA2 report file\n Kraken2 Krona Plot:\n text: Kraken2 Krona Plot\n description: Kraken2 krona plot HTML file\n Centrifuge Krona Plot:\n text: Centrifuge Krona Plot\n description: Centrifuge krona plot HTML file\n Centrifuge output report file:\n text: Centrifuge output report file\n description: Centrifuge output report file\n Kraken2 Classification Report:\n text: Kraken2 Classification Report\n description: Kraken2 output report file\n Kraken2 Taxonomic Classification:\n text: Kraken2 Taxonomic Classification\n description: Kraken2 output read classification file\n Centrifuge Classification Report:\n text: Centrifuge Classification Report\n description: Centrifuge output report file\n Centrifuge Taxonomic Classification:\n text: Centrifuge Taxonomic Classification\n description: Centrifuge output read classification file\n Structural Annotation GFF:\n text: Structural Annotation GFF\n description: GFF3 format file with structural annotations\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_structural_annotation.gff'\n Structural Annotation Stats Json:\n text: Structural Annotation Stats Json\n description: Structural annotations stats json\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_structural_annotation_stats.json'\n Functional Annotation GFF:\n text: Functional Annotation GFF\n description: GFF3 format file with functional annotations\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_functional_annotation.gff'\n Annotation Info File:\n text: Annotation Info File\n description: File containing annotation info\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_imgap.info'\n Annotation Amino Acid FASTA:\n text: Annotation Amino Acid FASTA\n description: FASTA amino acid file for annotated proteins\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_proteins.faa'\n Annotation Enzyme Commission:\n text: Annotation Enzyme Commission\n description: Tab delimited file for EC annotation\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ec.tsv'\n Annotation KEGG Orthology:\n text: Annotation KEGG Orthology\n description: Tab delimited file for KO annotation\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ko.tsv'\n Assembly Info File:\n text: Assembly Info File\n description: File containing assembly info\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: README.txt\n Assembly Coverage BAM:\n text: Assembly Coverage BAM\n description: Sorted bam file of reads mapping back to the final assembly\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pairedMapped.sam.gz'\n Assembly AGP:\n text: Assembly AGP\n description: An AGP format file that describes the assembly\n Assembly Scaffolds:\n text: Assembly Scaffolds\n description: Final assembly scaffolds fasta\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_assembly.contigs.fasta'\n Assembly Contigs:\n text: Assembly Contigs\n description: Final assembly contigs fasta\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: assembly.contigs.fasta\n Assembly Coverage Stats:\n text: Assembly Coverage Stats\n description: Assembled contigs coverage information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pairedMapped_sorted.bam.cov'\n Contig Mapping File:\n text: Contig Mapping File\n description: Contig mappings between contigs and scaffolds\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_contig_names_mapping.tsv'\n Error Corrected Reads:\n text: Error Corrected Reads\n description: Error corrected reads fastq\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: input.corr.fastq.gz\n Filtered Sequencing Reads:\n text: Filtered Sequencing Reads\n description: Reads QC result fastq (clean data)\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '/.+?(?=filter)/filter-METAGENOME.fastq.gz '\n Read Filtering Info File:\n text: Read Filtering Info File\n description: File containing read filtering information\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[rqc_wf_activity_id]_readsQC.info'\n QC Statistics Extended:\n text: QC Statistics Extended\n description: Extended report including methods and results for read filtering\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: /.+?(?=filter)/filtered-report.txt\n QC Statistics:\n text: QC Statistics\n description: Reads QC summary statistics\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[rqc_wf_activity_id]_filterStats2.txt'\n TIGRFam Annotation GFF:\n text: TIGRFam Annotation GFF\n description: GFF3 format file with TIGRfam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_tigrfam.gff'\n CRT Annotation GFF:\n text: CRT Annotation GFF\n description: GFF3 format file with CRT\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_crt.gff'\n Genemark Annotation GFF:\n text: Genemark Annotation GFF\n description: GFF3 format file with Genemark\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_genemark.gff'\n Prodigal Annotation GFF:\n text: Prodigal Annotation GFF\n description: GFF3 format file with Prodigal\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_prodigal.gff'\n TRNA Annotation GFF:\n text: TRNA Annotation GFF\n description: GFF3 format file with TRNA\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_trna.gff'\n Misc Annotation GFF:\n text: Misc Annotation GFF\n description: GFF3 format file with Misc\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam_misc_bind_misc_feature_regulatory.gff'\n RFAM Annotation GFF:\n text: RFAM Annotation GFF\n description: GFF3 format file with RFAM\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam.gff'\n TMRNA Annotation GFF:\n text: TMRNA Annotation GFF\n description: GFF3 format file with TMRNA\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_rfam_ncrna_tmrna.gff'\n Crispr Terms:\n text: Crispr Terms\n description: Crispr Terms\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_crt.crisprs'\n Product Names:\n text: Product Names\n description: Product names file\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_product_names.tsv'\n Gene Phylogeny tsv:\n text: Gene Phylogeny tsv\n description: Gene Phylogeny tsv\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_gene_phylogeny.tsv'\n Scaffold Lineage tsv:\n text: Scaffold Lineage tsv\n description: phylogeny at the scaffold level\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_scaffold_lineage.tsv'\n Clusters of Orthologous Groups (COG) Annotation GFF:\n text: Clusters of Orthologous Groups (COG) Annotation GFF\n description: GFF3 format file with COGs\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_cog.gff'\n KO_EC Annotation GFF:\n text: KO_EC Annotation GFF\n description: GFF3 format file with KO_EC\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_ko_ec.gff'\n CATH FunFams (Functional Families) Annotation GFF:\n text: CATH FunFams (Functional Families) Annotation GFF\n description: GFF3 format file with CATH FunFams\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_cath_funfam.gff'\n SUPERFam Annotation GFF:\n text: SUPERFam Annotation GFF\n description: GFF3 format file with SUPERFam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_supfam.gff'\n SMART Annotation GFF:\n text: SMART Annotation GFF\n description: GFF3 format file with SMART\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_smart.gff'\n Pfam Annotation GFF:\n text: Pfam Annotation GFF\n description: GFF3 format file with Pfam\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '[GOLD-AP]_pfam.gff'\n Annotation Statistics:\n text: Annotation Statistics\n description: Annotation statistics report\n Direct Infusion FT ICR-MS Raw Data:\n text: Direct Infusion FT ICR-MS Raw Data\n description: Direct infusion 21 Tesla Fourier Transform ion cyclotron resonance\n mass spectrometry raw data acquired in broadband full scan mode\n LC-DDA-MS/MS Raw Data:\n text: LC-DDA-MS/MS Raw Data\n description: Liquid chromatographically separated MS1 and Data-Dependent MS2 binary\n instrument file\n Configuration toml:\n text: Configuration toml\n description: A configuration toml file used by various programs to store settings\n that are specific to their respective software.\n broad_mappings:\n - edam.format:4005\n LC-MS Lipidomics Results:\n text: LC-MS Lipidomics Results\n description: LC-MS-based lipidomics analysis results table\n LC-MS Lipidomics Processed Data:\n text: LC-MS Lipidomics Processed Data\n description: Processed data for the LC-MS-based lipidomics analysis in hdf5 format\n Contaminants Amino Acid FASTA:\n text: Contaminants Amino Acid FASTA\n description: FASTA amino acid file for contaminant proteins commonly observed\n in proteomics data.\n Analysis Tool Parameter File:\n text: Analysis Tool Parameter File\n description: A configuration file used by a single computational software tool\n that stores settings that are specific to that tool.\n Workflow Operation Summary:\n text: Workflow Operation Summary\n description: A human readable record of analysis steps applied during an instance\n of a workflow operation.\n Metatranscriptome Expression:\n text: Metatranscriptome Expression\n description: Metatranscriptome expression values and read counts for gene features\n predicted on contigs\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*.rnaseq_gea.txt'\n Metatranscriptome Expression Intergenic:\n text: Metatranscriptome Expression Intergenic\n description: Metatranscriptome expression values and read counts for intergenic\n regions.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*.rnaseq_gea.intergenic.txt'\n Metatranscriptome Expression Info File:\n text: Metatranscriptome Expression Info File\n description: File containing version information on the expression workflow\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*_readcount.info'\n rRNA Filtered Sequencing Reads:\n text: rRNA Filtered Sequencing Reads\n description: File containing ribosomal reads from the read qc filtering step.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*.rRNA.fastq.gz'\n BAI File:\n text: BAI File\n description: An index file found in the same directory as the binary alignment\n map (BAM) file, a compressed binary version of a sequence alignment/map (SAM)\n file.\n annotations:\n file_name_pattern:\n tag: file_name_pattern\n value: '*.pairedMapped_sorted.bam.bai'\n exact_mappings:\n - NCIT:C190163\n\nURI: FilterTypeEnum
"},{"location":"FilterTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description particulate air filter None chemical air filter None low-MERV pleated media None HEPA None electrostatic None gas-phase or ultraviolet air treatments None"},{"location":"FilterTypeEnum/#slots","title":"Slots","text":"Name Description filter_type A device which removes solid particulates or airborne molecular contaminants"},{"location":"FilterTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FilterTypeEnum/#schema-source","title":"Schema Source","text":"name: filter_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n particulate air filter:\n text: particulate air filter\n chemical air filter:\n text: chemical air filter\n low-MERV pleated media:\n text: low-MERV pleated media\n HEPA:\n text: HEPA\n electrostatic:\n text: electrostatic\n gas-phase or ultraviolet air treatments:\n text: gas-phase or ultraviolet air treatments\n\nThe process of segregation of phases; e.g. the separation of suspended solids from a liquid or gas, usually by forcing a carrier gas or liquid through a porous medium.
URI: nmdc:FiltrationProcess
classDiagram\n class FiltrationProcess\n click FiltrationProcess href \"../FiltrationProcess\"\n MaterialProcessing <|-- FiltrationProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n FiltrationProcess : alternative_identifiers\n\n FiltrationProcess : conditionings\n\n FiltrationProcess : container_size\n\n FiltrationProcess --> \"0..1\" QuantityValue : container_size\n click QuantityValue href \"../QuantityValue\"\n\n FiltrationProcess : description\n\n FiltrationProcess : end_date\n\n FiltrationProcess : filter_material\n\n FiltrationProcess : filter_pore_size\n\n FiltrationProcess --> \"0..1\" QuantityValue : filter_pore_size\n click QuantityValue href \"../QuantityValue\"\n\n FiltrationProcess : filtration_category\n\n FiltrationProcess : has_failure_categorization\n\n FiltrationProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n FiltrationProcess : has_input\n\n FiltrationProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n FiltrationProcess : has_output\n\n FiltrationProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n FiltrationProcess : id\n\n FiltrationProcess : instrument_used\n\n FiltrationProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n FiltrationProcess : is_pressurized\n\n FiltrationProcess : name\n\n FiltrationProcess : processing_institution\n\n FiltrationProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n FiltrationProcess : protocol_link\n\n FiltrationProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n FiltrationProcess : qc_comment\n\n FiltrationProcess : qc_status\n\n FiltrationProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n FiltrationProcess : separation_method\n\n FiltrationProcess --> \"0..1\" SeparationMethodEnum : separation_method\n click SeparationMethodEnum href \"../SeparationMethodEnum\"\n\n FiltrationProcess : start_date\n\n FiltrationProcess : type\n\n FiltrationProcess : volume\n\n FiltrationProcess --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: FiltrationProcess\ndescription: The process of segregation of phases; e.g. the separation of suspended\n solids from a liquid or gas, usually by forcing a carrier gas or liquid through\n a porous medium.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- CHMO:0001640\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslots:\n- conditionings\n- container_size\n- filter_material\n- filter_pore_size\n- filtration_category\n- is_pressurized\n- separation_method\n- volume\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The volume of sample filtered.\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:FiltrationProcess\n\nname: FiltrationProcess\ndescription: The process of segregation of phases; e.g. the separation of suspended\n solids from a liquid or gas, usually by forcing a carrier gas or liquid through\n a porous medium.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- CHMO:0001640\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The volume of sample filtered.\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n conditionings:\n name: conditionings\n description: Preliminary treatment of either phase with a suitable solution of\n the other phase (in the absence of main extractable solute(s)) so that when\n the subsequent equilibration is carried out changes in the (volume) phase ratio\n or in the concentrations of other components are minimized.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n list_elements_ordered: true\n alias: conditionings\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: string\n multivalued: true\n container_size:\n name: container_size\n description: The volume of the container an analyte is stored in or an activity\n takes place in\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: container_size\n owner: FiltrationProcess\n domain_of:\n - SubSamplingProcess\n - FiltrationProcess\n range: QuantityValue\n filter_material:\n name: filter_material\n description: A porous material on which solid particles present in air or other\n fluid which flows through it are largely caught and retained.\n comments:\n - 'Filters are made with a variety of materials: cellulose and derivatives, glass\n fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous\n or be made so by mechanical or other means. Membrane/ceramic filters are prepared\n with highly controlled pore size in a sheet of suitable material such as polyfluoroethylene,\n polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement.\n The pores constitute 80\u201385% of the filter volume commonly and several pore sizes\n are available for air sampling (0.45\u22120.8 \u03bcm are commonly employed).'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: filter_material\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: string\n filter_pore_size:\n name: filter_pore_size\n description: A quantitative or qualitative measurement of the physical dimensions\n of the pores in a material.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: filter_pore_size\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: QuantityValue\n filtration_category:\n name: filtration_category\n description: The type of conditioning applied to a filter, device, etc.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: filtration_category\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: string\n is_pressurized:\n name: is_pressurized\n description: Whether or not pressure was applied to a thing or process.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_pressurized\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: boolean\n separation_method:\n name: separation_method\n description: The method that was used to separate a substance from a solution\n or mixture.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: separation_method\n owner: FiltrationProcess\n domain_of:\n - FiltrationProcess\n range: SeparationMethodEnum\n volume:\n name: volume\n description: The volume of sample filtered.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: FiltrationProcess\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: FiltrationProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: FiltrationProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: FiltrationProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:filtpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FiltrationProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FiltrationProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: FiltrationProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FiltrationProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FiltrationProcess\n\nA real number that conforms to the xsd:float specification
URI: xsd:float
base: float
uri: xsd:float
URI: FloorCondEnum
"},{"location":"FloorCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"FloorCondEnum/#slots","title":"Slots","text":"Name Description floor_cond The physical condition of the floor at the time of sampling; photos or video ..."},{"location":"FloorCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorCondEnum/#schema-source","title":"Schema Source","text":"name: floor_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nURI: FloorFinishMatEnum
"},{"location":"FloorFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description tile None wood strip or parquet None carpet None rug None laminate wood None lineoleum None vinyl composition tile None sheet vinyl None stone None bamboo None cork None terrazo None concrete None none None sealed None clear finish None paint None none or unfinished None"},{"location":"FloorFinishMatEnum/#slots","title":"Slots","text":"Name Description floor_finish_mat The floor covering type; the finished surface that is walked on"},{"location":"FloorFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorFinishMatEnum/#schema-source","title":"Schema Source","text":"name: floor_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n tile:\n text: tile\n wood strip or parquet:\n text: wood strip or parquet\n carpet:\n text: carpet\n rug:\n text: rug\n laminate wood:\n text: laminate wood\n lineoleum:\n text: lineoleum\n vinyl composition tile:\n text: vinyl composition tile\n sheet vinyl:\n text: sheet vinyl\n stone:\n text: stone\n bamboo:\n text: bamboo\n cork:\n text: cork\n terrazo:\n text: terrazo\n concrete:\n text: concrete\n none:\n text: none\n sealed:\n text: sealed\n clear finish:\n text: clear finish\n paint:\n text: paint\n none or unfinished:\n text: none or unfinished\n\nURI: FloorStrucEnum
"},{"location":"FloorStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description balcony None floating floor None glass floor None raised floor None sprung floor None wood-framed None concrete None"},{"location":"FloorStrucEnum/#slots","title":"Slots","text":"Name Description floor_struc Refers to the structural elements and subfloor upon which the finish flooring..."},{"location":"FloorStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorStrucEnum/#schema-source","title":"Schema Source","text":"name: floor_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n balcony:\n text: balcony\n floating floor:\n text: floating floor\n glass floor:\n text: glass floor\n raised floor:\n text: raised floor\n sprung floor:\n text: sprung floor\n wood-framed:\n text: wood-framed\n concrete:\n text: concrete\n\nURI: FloorWaterMoldEnum
"},{"location":"FloorWaterMoldEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mold odor None wet floor None water stains None wall discoloration None floor discoloration None ceiling discoloration None peeling paint or wallpaper None bulging walls None condensation None"},{"location":"FloorWaterMoldEnum/#slots","title":"Slots","text":"Name Description floor_water_mold Signs of the presence of mold or mildew in a room"},{"location":"FloorWaterMoldEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FloorWaterMoldEnum/#schema-source","title":"Schema Source","text":"name: floor_water_mold_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n mold odor:\n text: mold odor\n wet floor:\n text: wet floor\n water stains:\n text: water stains\n wall discoloration:\n text: wall discoloration\n floor discoloration:\n text: floor discoloration\n ceiling discoloration:\n text: ceiling discoloration\n peeling paint or wallpaper:\n text: peeling paint or wallpaper\n bulging walls:\n text: bulging walls\n condensation:\n text: condensation\n\nURI: FreqCleanEnum
"},{"location":"FreqCleanEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Daily None Weekly None Monthly None Quarterly None Annually None other None"},{"location":"FreqCleanEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FreqCleanEnum/#schema-source","title":"Schema Source","text":"name: freq_clean_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Daily:\n text: Daily\n Weekly:\n text: Weekly\n Monthly:\n text: Monthly\n Quarterly:\n text: Quarterly\n Annually:\n text: Annually\n other:\n text: other\n\nAn assignment of a function term (e.g. reaction or pathway) that is executed by a gene product, or which the gene product plays an active role in. Functional annotations can be assigned manually by curators, or automatically in workflows. In the context of NMDC, all function annotation is performed automatically, typically using HMM or Blast type methods
URI: nmdc:FunctionalAnnotation
classDiagram\n class FunctionalAnnotation\n click FunctionalAnnotation href \"../FunctionalAnnotation\"\n\n FunctionalAnnotation : feature_category\n\n FunctionalAnnotation --> \"0..1\" ControlledIdentifiedTermValue : feature_category\n click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n FunctionalAnnotation : has_function\n\n FunctionalAnnotation : subject\n\n FunctionalAnnotation --> \"0..1\" GeneProduct : subject\n click GeneProduct href \"../GeneProduct\"\n\n FunctionalAnnotation : type\n\n FunctionalAnnotation : was_generated_by\n\n FunctionalAnnotation --> \"0..1\" MetagenomeAnnotation : was_generated_by\n click MetagenomeAnnotation href \"../MetagenomeAnnotation\"\n\n\n\nname: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n by a gene product, or which the gene product plays an active role in. Functional\n annotations can be assigned manually by curators, or automatically in workflows. In\n the context of NMDC, all function annotation is performed automatically, typically\n using HMM or Blast type methods\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslots:\n- has_function\n- subject\n- was_generated_by\n- type\n- feature_category\nslot_usage:\n has_function:\n name: has_function\n notes:\n - Still missing patterns for COG and RetroRules\n - These patterns are not yet tied to the listed prefixes. A discussion about that\n possibility had been started, including the question of whether these lists\n are intended to be open examples or closed\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n range: MetagenomeAnnotation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\nclass_uri: nmdc:FunctionalAnnotation\n\nname: FunctionalAnnotation\ndescription: An assignment of a function term (e.g. reaction or pathway) that is executed\n by a gene product, or which the gene product plays an active role in. Functional\n annotations can be assigned manually by curators, or automatically in workflows. In\n the context of NMDC, all function annotation is performed automatically, typically\n using HMM or Blast type methods\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://img.jgi.doe.gov/docs/functional-annotation.pdf\n- https://github.com/microbiomedata/mg_annotation/blob/master/functional-annotation.wdl\nnarrow_mappings:\n- biolink:GeneToGoTermAssociation\nslot_usage:\n has_function:\n name: has_function\n notes:\n - Still missing patterns for COG and RetroRules\n - These patterns are not yet tied to the listed prefixes. A discussion about that\n possibility had been started, including the question of whether these lists\n are intended to be open examples or closed\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n range: MetagenomeAnnotation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\nattributes:\n has_function:\n name: has_function\n notes:\n - Still missing patterns for COG and RetroRules\n - These patterns are not yet tied to the listed prefixes. A discussion about that\n possibility had been started, including the question of whether these lists\n are intended to be open examples or closed\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_function\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotation\n range: string\n pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n subject:\n name: subject\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: subject\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotation\n - OntologyRelation\n range: GeneProduct\n was_generated_by:\n name: was_generated_by\n description: provenance for the annotation.\n notes:\n - To be consistent with the rest of the NMDC schema we use the PROV annotation\n model, rather than GPAD\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: FunctionalAnnotation\n domain_of:\n - FunctionalAnnotationAggMember\n - FunctionalAnnotation\n - DataObject\n range: MetagenomeAnnotation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n any_of:\n - range: WorkflowExecution\n - range: DataGeneration\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FunctionalAnnotation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n feature_category:\n name: feature_category\n description: A Sequence Ontology term that describes the category of a feature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: feature_category\n owner: FunctionalAnnotation\n domain_of:\n - GenomeFeature\n - FunctionalAnnotation\n range: ControlledIdentifiedTermValue\nclass_uri: nmdc:FunctionalAnnotation\n\nURI: nmdc:FunctionalAnnotationAggMember
classDiagram\n class FunctionalAnnotationAggMember\n click FunctionalAnnotationAggMember href \"../FunctionalAnnotationAggMember\"\n\n FunctionalAnnotationAggMember : count\n\n FunctionalAnnotationAggMember : gene_function_id\n\n FunctionalAnnotationAggMember : type\n\n FunctionalAnnotationAggMember : was_generated_by\n\n FunctionalAnnotationAggMember --> \"1\" WorkflowExecution : was_generated_by\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\nname: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- was_generated_by\n- gene_function_id\n- count\n- type\nslot_usage:\n was_generated_by:\n name: was_generated_by\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan|wfmp|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n count:\n name: count\n description: The number of sequences (for a metagenome or metatranscriptome) or\n spectra (for metaproteomics) associated with the specified function.\nclass_uri: nmdc:FunctionalAnnotationAggMember\n\nname: FunctionalAnnotationAggMember\nfrom_schema: https://w3id.org/nmdc/nmdc\nslot_usage:\n was_generated_by:\n name: was_generated_by\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan|wfmp|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n count:\n name: count\n description: The number of sequences (for a metagenome or metatranscriptome) or\n spectra (for metaproteomics) associated with the specified function.\nattributes:\n was_generated_by:\n name: was_generated_by\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:wasGeneratedBy\n rank: 1000\n alias: was_generated_by\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n - FunctionalAnnotation\n - DataObject\n range: WorkflowExecution\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(wfmgan|wfmp|wfmtan)-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n any_of:\n - range: WorkflowExecution\n - range: DataGeneration\n gene_function_id:\n name: gene_function_id\n description: The identifier for the gene function.\n examples:\n - value: KEGG.ORTHOLOGY:K00627\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gene_function_id\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: uriorcurie\n required: true\n count:\n name: count\n description: The number of sequences (for a metagenome or metatranscriptome) or\n spectra (for metaproteomics) associated with the specified function.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: count\n owner: FunctionalAnnotationAggMember\n domain_of:\n - FunctionalAnnotationAggMember\n range: integer\n required: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FunctionalAnnotationAggMember\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FunctionalAnnotationAggMember\n\nAbstract grouping class for any term/descriptor that can be applied to a functional unit of a genome (protein, ncRNA, complex).
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:FunctionalAnnotationTerm
classDiagram\n class FunctionalAnnotationTerm\n click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n OntologyClass <|-- FunctionalAnnotationTerm\n click OntologyClass href \"../OntologyClass\"\n\n\n FunctionalAnnotationTerm <|-- Pathway\n click Pathway href \"../Pathway\"\n FunctionalAnnotationTerm <|-- OrthologyGroup\n click OrthologyGroup href \"../OrthologyGroup\"\n\n\n\n FunctionalAnnotationTerm : alternative_identifiers\n\n FunctionalAnnotationTerm : alternative_names\n\n FunctionalAnnotationTerm : definition\n\n FunctionalAnnotationTerm : description\n\n FunctionalAnnotationTerm : id\n\n FunctionalAnnotationTerm : name\n\n FunctionalAnnotationTerm : relations\n\n FunctionalAnnotationTerm --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n FunctionalAnnotationTerm : type\n\n\n\nname: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming (Duncan, 2021-04-02)\n- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup\n subclasses.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nclass_uri: nmdc:FunctionalAnnotationTerm\n\nname: FunctionalAnnotationTerm\ndescription: Abstract grouping class for any term/descriptor that can be applied to\n a functional unit of a genome (protein, ncRNA, complex).\ntodos:\n- decide if this should be used for product naming (Duncan, 2021-04-02)\n- Retaining this even after removing Reaction. See todos on the Pathway and OrthologyGroup\n subclasses.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- function\n- FunctionalAnnotation\nis_a: OntologyClass\nabstract: true\nattributes:\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: FunctionalAnnotationTerm\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: FunctionalAnnotationTerm\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: FunctionalAnnotationTerm\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: FunctionalAnnotationTerm\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: FunctionalAnnotationTerm\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: FunctionalAnnotationTerm\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: FunctionalAnnotationTerm\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: FunctionalAnnotationTerm\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:FunctionalAnnotationTerm\n\nURI: FurnitureEnum
"},{"location":"FurnitureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None chair None desks None"},{"location":"FurnitureEnum/#slots","title":"Slots","text":"Name Description furniture The types of furniture present in the sampled room"},{"location":"FurnitureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"FurnitureEnum/#schema-source","title":"Schema Source","text":"name: furniture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cabinet:\n text: cabinet\n chair:\n text: chair\n desks:\n text: desks\n\nURI: GenderRestroomEnum
"},{"location":"GenderRestroomEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description all gender None female None gender neurtral None male None male and female None unisex None"},{"location":"GenderRestroomEnum/#slots","title":"Slots","text":"Name Description gender_restroom The gender type of the restroom"},{"location":"GenderRestroomEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GenderRestroomEnum/#schema-source","title":"Schema Source","text":"name: gender_restroom_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n all gender:\n text: all gender\n female:\n text: female\n gender neurtral:\n text: gender neurtral\n male:\n text: male\n male and female:\n text: male and female\n unisex:\n text: unisex\n\nA molecule encoded by a gene that has an evolved function
URI: nmdc:GeneProduct
classDiagram\n class GeneProduct\n click GeneProduct href \"../GeneProduct\"\n NamedThing <|-- GeneProduct\n click NamedThing href \"../NamedThing\"\n\n\n\n GeneProduct : alternative_identifiers\n\n GeneProduct : description\n\n GeneProduct : id\n\n GeneProduct : name\n\n GeneProduct : type\n\n\n\nInstances of this class should have identifiers with one of the following prefixes:
PR
UniProtKB
gtpo
name: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nclass_uri: nmdc:GeneProduct\n\nname: GeneProduct\nid_prefixes:\n- PR\n- UniProtKB\n- gtpo\ndescription: A molecule encoded by a gene that has an evolved function\nnotes:\n- we may include a more general gene product class in future to allow for ncRNA annotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneProduct\nis_a: NamedThing\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: GeneProduct\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: GeneProduct\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: GeneProduct\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: GeneProduct\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: GeneProduct\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:GeneProduct\n\nA feature localized to an interval along a genome
URI: nmdc:GenomeFeature
classDiagram\n class GenomeFeature\n click GenomeFeature href \"../GenomeFeature\"\n\n GenomeFeature : encodes\n\n GenomeFeature --> \"0..1\" GeneProduct : encodes\n click GeneProduct href \"../GeneProduct\"\n\n GenomeFeature : end\n\n GenomeFeature : feature_category\n\n GenomeFeature --> \"0..1\" ControlledIdentifiedTermValue : feature_category\n click ControlledIdentifiedTermValue href \"../ControlledIdentifiedTermValue\"\n\n GenomeFeature : feature_type\n\n GenomeFeature : phase\n\n GenomeFeature : seqid\n\n GenomeFeature : start\n\n GenomeFeature : strand\n\n GenomeFeature : type\n\n\n\nname: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslots:\n- encodes\n- end\n- feature_type\n- phase\n- seqid\n- start\n- strand\n- type\n- feature_category\nslot_usage:\n seqid:\n name: seqid\n required: true\n start:\n name: start\n required: true\n end:\n name: end\n required: true\nclass_uri: nmdc:GenomeFeature\n\nname: GenomeFeature\ndescription: A feature localized to an interval along a genome\ncomments:\n- corresponds to an entry in GFF3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md\nslot_usage:\n seqid:\n name: seqid\n required: true\n start:\n name: start\n required: true\n end:\n name: end\n required: true\nattributes:\n encodes:\n name: encodes\n description: The gene product encoded by this feature. Typically this is used\n for a CDS feature or gene feature which will encode a protein. It can also be\n used by a nc transcript ot gene feature that encoded a ncRNA\n todos:\n - If we revert Reaction back into the schema, that would be a reasonable domain\n for this slot\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: encodes\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: GeneProduct\n end:\n name: end\n description: The end of the feature in positive 1-based integer coordinates\n comments:\n - '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n feature, end = the position of the end + the length of the landmark feature.\"'\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - biolink:end_interbase_coordinate\n rank: 1000\n is_a: gff_coordinate\n alias: end\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n required: true\n minimum_value: 1\n feature_type:\n name: feature_type\n description: 'TODO: Yuri to write'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: feature_type\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n phase:\n name: phase\n description: The phase for a coding sequence entity. For example, phase of a CDS\n as represented in a GFF3 with a value of 0, 1 or 2.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - biolink:phase\n rank: 1000\n alias: phase\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n minimum_value: 0\n maximum_value: 2\n seqid:\n name: seqid\n description: The ID of the landmark used to establish the coordinate system for\n the current feature.\n todos:\n - change range from string to object\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: seqid\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n required: true\n start:\n name: start\n description: The start of the feature in positive 1-based integer coordinates\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - biolink:start_interbase_coordinate\n rank: 1000\n is_a: gff_coordinate\n alias: start\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: integer\n required: true\n minimum_value: 1\n strand:\n name: strand\n description: The strand on which a feature is located. Has a value of '+' (sense\n strand or forward strand) or '-' (anti-sense strand or reverse strand).\n todos:\n - set the range to an enum?\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - biolink:strand\n rank: 1000\n alias: strand\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: GenomeFeature\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n feature_category:\n name: feature_category\n description: A Sequence Ontology term that describes the category of a feature\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: feature_category\n owner: GenomeFeature\n domain_of:\n - GenomeFeature\n - FunctionalAnnotation\n range: ControlledIdentifiedTermValue\nclass_uri: nmdc:GenomeFeature\n\nA normalized value for a location on the earth's surface
URI: nmdc:GeolocationValue
classDiagram\n class GeolocationValue\n click GeolocationValue href \"../GeolocationValue\"\n AttributeValue <|-- GeolocationValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n GeolocationValue : has_raw_value\n\n GeolocationValue : latitude\n\n GeolocationValue : longitude\n\n GeolocationValue : type\n\n\n\nname: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslots:\n- latitude\n- longitude\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n latitude:\n name: latitude\n required: true\n longitude:\n name: longitude\n required: true\nclass_uri: nmdc:GeolocationValue\n\nname: GeolocationValue\ndescription: A normalized value for a location on the earth's surface\nnotes:\n- 'what did ''to_str: {latitude} {longitude}'' mean?'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:GeoCoordinates\nis_a: AttributeValue\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n latitude:\n name: latitude\n required: true\n longitude:\n name: longitude\n required: true\nattributes:\n latitude:\n name: latitude\n description: latitude\n examples:\n - value: '-33.460524'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - schema:latitude\n rank: 1000\n slot_uri: wgs84:lat\n alias: latitude\n owner: GeolocationValue\n domain_of:\n - GeolocationValue\n range: decimal_degree\n required: true\n longitude:\n name: longitude\n description: longitude\n examples:\n - value: '150.168149'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - schema:longitude\n rank: 1000\n slot_uri: wgs84:long\n alias: longitude\n owner: GeolocationValue\n domain_of:\n - GeolocationValue\n range: decimal_degree\n required: true\n has_raw_value:\n name: has_raw_value\n description: The raw value for a geolocation should follow {latitude} {longitude}\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: GeolocationValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: GeolocationValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:GeolocationValue\n\nURI: GrowthHabitEnum
"},{"location":"GrowthHabitEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description erect None semi-erect None spreading None prostrate None"},{"location":"GrowthHabitEnum/#slots","title":"Slots","text":"Name Description growth_habit Characteristic shape, appearance or growth form of a plant species"},{"location":"GrowthHabitEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"GrowthHabitEnum/#schema-source","title":"Schema Source","text":"name: growth_habit_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n erect:\n text: erect\n semi-erect:\n text: semi-erect\n spreading:\n text: spreading\n prostrate:\n text: prostrate\n\nURI: HandidnessEnum
"},{"location":"HandidnessEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ambidexterity None left handedness None mixed-handedness None right handedness None"},{"location":"HandidnessEnum/#slots","title":"Slots","text":"Name Description handidness The handidness of the individual sampled"},{"location":"HandidnessEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HandidnessEnum/#schema-source","title":"Schema Source","text":"name: handidness_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n ambidexterity:\n text: ambidexterity\n left handedness:\n text: left handedness\n mixed-handedness:\n text: mixed-handedness\n right handedness:\n text: right handedness\n\nURI: HcProducedEnum
"},{"location":"HcProducedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil None Gas-Condensate None Gas None Bitumen None Coalbed Methane None other None"},{"location":"HcProducedEnum/#slots","title":"Slots","text":"Name Description hc_produced Main hydrocarbon type produced from resource (i"},{"location":"HcProducedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcProducedEnum/#schema-source","title":"Schema Source","text":"name: hc_produced_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Oil:\n text: Oil\n Gas-Condensate:\n text: Gas-Condensate\n Gas:\n text: Gas\n Bitumen:\n text: Bitumen\n Coalbed Methane:\n text: Coalbed Methane\n other:\n text: other\n\nURI: HcrEnum
"},{"location":"HcrEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Oil Reservoir None Gas Reservoir None Oil Sand None Coalbed None Shale None Tight Oil Reservoir None Tight Gas Reservoir None other None"},{"location":"HcrEnum/#slots","title":"Slots","text":"Name Description hcr Main Hydrocarbon Resource type"},{"location":"HcrEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrEnum/#schema-source","title":"Schema Source","text":"name: hcr_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Oil Reservoir:\n text: Oil Reservoir\n Gas Reservoir:\n text: Gas Reservoir\n Oil Sand:\n text: Oil Sand\n Coalbed:\n text: Coalbed\n Shale:\n text: Shale\n Tight Oil Reservoir:\n text: Tight Oil Reservoir\n Tight Gas Reservoir:\n text: Tight Gas Reservoir\n other:\n text: other\n\nURI: HcrGeolAgeEnum
"},{"location":"HcrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"HcrGeolAgeEnum/#slots","title":"Slots","text":"Name Description hcr_geol_age Geological age of hydrocarbon resource (Additional info: https://en"},{"location":"HcrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HcrGeolAgeEnum/#schema-source","title":"Schema Source","text":"name: hcr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Archean:\n text: Archean\n Cambrian:\n text: Cambrian\n Carboniferous:\n text: Carboniferous\n Cenozoic:\n text: Cenozoic\n Cretaceous:\n text: Cretaceous\n Devonian:\n text: Devonian\n Jurassic:\n text: Jurassic\n Mesozoic:\n text: Mesozoic\n Neogene:\n text: Neogene\n Ordovician:\n text: Ordovician\n Paleogene:\n text: Paleogene\n Paleozoic:\n text: Paleozoic\n Permian:\n text: Permian\n Precambrian:\n text: Precambrian\n Proterozoic:\n text: Proterozoic\n Silurian:\n text: Silurian\n Triassic:\n text: Triassic\n other:\n text: other\n\nURI: HeatCoolTypeEnum
"},{"location":"HeatCoolTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description radiant system None heat pump None forced air system None steam forced heat None wood stove None"},{"location":"HeatCoolTypeEnum/#slots","title":"Slots","text":"Name Description heat_cool_type Methods of conditioning or heating a room or building"},{"location":"HeatCoolTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatCoolTypeEnum/#schema-source","title":"Schema Source","text":"name: heat_cool_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n radiant system:\n text: radiant system\n heat pump:\n text: heat pump\n forced air system:\n text: forced air system\n steam forced heat:\n text: steam forced heat\n wood stove:\n text: wood stove\n\nURI: HeatDelivLocEnum
"},{"location":"HeatDelivLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"HeatDelivLocEnum/#slots","title":"Slots","text":"Name Description heat_deliv_loc The location of heat delivery within the room"},{"location":"HeatDelivLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HeatDelivLocEnum/#schema-source","title":"Schema Source","text":"name: heat_deliv_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: HostSexEnum
"},{"location":"HostSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description female None hermaphrodite None non-binary None male None transgender None transgender (female to male) None transgender (male to female) None undeclared None"},{"location":"HostSexEnum/#slots","title":"Slots","text":"Name Description host_sex Gender or physical sex of the host"},{"location":"HostSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"HostSexEnum/#schema-source","title":"Schema Source","text":"name: host_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n female:\n text: female\n hermaphrodite:\n text: hermaphrodite\n non-binary:\n text: non-binary\n male:\n text: male\n transgender:\n text: transgender\n transgender (female to male):\n text: transgender (female to male)\n transgender (male to female):\n text: transgender (male to female)\n undeclared:\n text: undeclared\n\nAn attribute value representing an image.
URI: nmdc:ImageValue
classDiagram\n class ImageValue\n click ImageValue href \"../ImageValue\"\n AttributeValue <|-- ImageValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n ImageValue : description\n\n ImageValue : display_order\n\n ImageValue : has_raw_value\n\n ImageValue : type\n\n ImageValue : url\n\n\n\nname: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- url\n- description\n- display_order\nclass_uri: nmdc:ImageValue\n\nname: ImageValue\ndescription: An attribute value representing an image.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: url\n owner: ImageValue\n domain_of:\n - ImageValue\n - Protocol\n - DataObject\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ImageValue\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n display_order:\n name: display_order\n description: When rendering information, this attribute to specify the order in\n which the information should be rendered.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: display_order\n owner: ImageValue\n domain_of:\n - ImageValue\n range: integer\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: ImageValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ImageValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ImageValue\n\nURI: IndoorSpaceEnum
"},{"location":"IndoorSpaceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bedroom None office None bathroom None foyer None kitchen None locker room None hallway None elevator None"},{"location":"IndoorSpaceEnum/#slots","title":"Slots","text":"Name Description indoor_space A distinguishable space within a structure, the purpose for which discrete ar..."},{"location":"IndoorSpaceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSpaceEnum/#schema-source","title":"Schema Source","text":"name: indoor_space_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bedroom:\n text: bedroom\n office:\n text: office\n bathroom:\n text: bathroom\n foyer:\n text: foyer\n kitchen:\n text: kitchen\n locker room:\n text: locker room\n hallway:\n text: hallway\n elevator:\n text: elevator\n\nURI: IndoorSurfEnum
"},{"location":"IndoorSurfEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description cabinet None ceiling None counter top None door None shelving None vent cover None window None wall None"},{"location":"IndoorSurfEnum/#slots","title":"Slots","text":"Name Description indoor_surf Type of indoor surface"},{"location":"IndoorSurfEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IndoorSurfEnum/#schema-source","title":"Schema Source","text":"name: indoor_surf_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n cabinet:\n text: cabinet\n ceiling:\n text: ceiling\n counter top:\n text: counter top\n door:\n text: door\n shelving:\n text: shelving\n vent cover:\n text: vent cover\n window:\n text: window\n wall:\n text: wall\n\nAny data or knowledge that reduces uncertainty or enhances understanding about a system, process, or entity.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:InformationObject
classDiagram\n class InformationObject\n click InformationObject href \"../InformationObject\"\n NamedThing <|-- InformationObject\n click NamedThing href \"../NamedThing\"\n\n\n InformationObject <|-- Configuration\n click Configuration href \"../Configuration\"\n InformationObject <|-- Manifest\n click Manifest href \"../Manifest\"\n InformationObject <|-- CalibrationInformation\n click CalibrationInformation href \"../CalibrationInformation\"\n InformationObject <|-- DataObject\n click DataObject href \"../DataObject\"\n\n\n\n InformationObject : alternative_identifiers\n\n InformationObject : description\n\n InformationObject : id\n\n InformationObject : name\n\n InformationObject : type\n\n\n\nname: InformationObject\ndescription: Any data or knowledge that reduces uncertainty or enhances understanding\n about a system, process, or entity.\ncomments:\n- The direct subclasses of NamedThing should aggregate the relevant classes and make\n them uniform. PlannedProcess and MaterialEntity are clearly disjoint. Let's do the\n same thing for our modelling of things that don't consist of matter and aren't processes.\n- InformationObjects may include embedded data or links to external resources via\n the url slot\n- May appear as output from a process, inputs into a process, or both\n- All slots relating one class to a InformationObject should be is_a sub-properties\n of has_input or has_output, if they are multivalued or otherwise organized\n- Historically information about many classes has been inlined into the class. This\n is an alternative pattern.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:AttributeValue\nis_a: NamedThing\nabstract: true\nclass_uri: nmdc:InformationObject\n\nname: InformationObject\ndescription: Any data or knowledge that reduces uncertainty or enhances understanding\n about a system, process, or entity.\ncomments:\n- The direct subclasses of NamedThing should aggregate the relevant classes and make\n them uniform. PlannedProcess and MaterialEntity are clearly disjoint. Let's do the\n same thing for our modelling of things that don't consist of matter and aren't processes.\n- InformationObjects may include embedded data or links to external resources via\n the url slot\n- May appear as output from a process, inputs into a process, or both\n- All slots relating one class to a InformationObject should be is_a sub-properties\n of has_input or has_output, if they are multivalued or otherwise organized\n- Historically information about many classes has been inlined into the class. This\n is an alternative pattern.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:AttributeValue\nis_a: NamedThing\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: InformationObject\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: InformationObject\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: InformationObject\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: InformationObject\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: InformationObject\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:InformationObject\n\nA material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
URI: nmdc:Instrument
classDiagram\n class Instrument\n click Instrument href \"../Instrument\"\n MaterialEntity <|-- Instrument\n click MaterialEntity href \"../MaterialEntity\"\n\n\n\n Instrument : alternative_identifiers\n\n Instrument : description\n\n Instrument : id\n\n Instrument : model\n\n Instrument --> \"0..1\" InstrumentModelEnum : model\n click InstrumentModelEnum href \"../InstrumentModelEnum\"\n\n Instrument : name\n\n Instrument : type\n\n Instrument : vendor\n\n Instrument --> \"0..1\" InstrumentVendorEnum : vendor\n click InstrumentVendorEnum href \"../InstrumentVendorEnum\"\n\n\n\nname: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n investigation, but is not a reagent.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000968\nis_a: MaterialEntity\nslots:\n- vendor\n- model\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:Instrument\n\nname: Instrument\ndescription: A material entity that is designed to perform a function in a scientific\n investigation, but is not a reagent.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- device\nexact_mappings:\n- OBI:0000968\nis_a: MaterialEntity\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n vendor:\n name: vendor\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: vendor\n owner: Instrument\n domain_of:\n - Instrument\n range: InstrumentVendorEnum\n model:\n name: model\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: model\n owner: Instrument\n domain_of:\n - Instrument\n range: InstrumentModelEnum\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Instrument\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Instrument\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Instrument\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Instrument\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Instrument\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Instrument\n\nURI: InstrumentModelEnum
"},{"location":"InstrumentModelEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description exploris_21T None exploris_240 None exploris_480 None ltq_orbitrap_velos None orbitrap_fusion_lumos None orbitrap_eclipse_tribid None orbitrap_q_exactive None solarix_7T None solarix_12T None solarix_15T None agilent_8890A None agilent_7980A None vortex_genie_2 None novaseq None novaseq_6000 OBI:0002630 novaseq_x None hiseq None hiseq_1000 OBI:0002022 hiseq_1500 OBI:0003386 hiseq_2000 OBI:0002001 hiseq_2500 OBI:0002002 hiseq_3000 OBI:0002048 hiseq_4000 OBI:0002049 hiseq_x_ten OBI:0002129 miniseq OBI:0003114 miseq OBI:0002003 nextseq_1000 OBI:0003606 nextseq None nextseq_500 OBI:0002021 nextseq_550 OBI:0003387 gridion OBI:0002751 minion OBI:0002750 promethion OBI:0002752 rs_II OBI:0002012 sequel OBI:0002632 sequel_II OBI:0002633 revio None"},{"location":"InstrumentModelEnum/#slots","title":"Slots","text":"Name Description model"},{"location":"InstrumentModelEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InstrumentModelEnum/#schema-source","title":"Schema Source","text":"name: InstrumentModelEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n exploris_21T:\n text: exploris_21T\n aliases:\n - Exploris 21T\n exploris_240:\n text: exploris_240\n aliases:\n - Orbitrap Exploris 240\n exploris_480:\n text: exploris_480\n aliases:\n - Orbitrap Exploris 480\n ltq_orbitrap_velos:\n text: ltq_orbitrap_velos\n aliases:\n - LTQ Orbitrap Velos\n - LTQ Orbitrap Velos ETD\n - Velos\n orbitrap_fusion_lumos:\n text: orbitrap_fusion_lumos\n aliases:\n - Orbitrap Fusion Lumos\n - Fusion\n orbitrap_eclipse_tribid:\n text: orbitrap_eclipse_tribid\n aliases:\n - Orbitrap Eclipse Tribid\n - Eclipse\n orbitrap_q_exactive:\n text: orbitrap_q_exactive\n aliases:\n - Orbitrap Q-Exactive HF\n - Orbitrap Q-Exactive HF-X\n solarix_7T:\n text: solarix_7T\n aliases:\n - 7T Solarix\n - 7T FT-ICR MS\n - 7T MRMS\n solarix_12T:\n text: solarix_12T\n aliases:\n - 12T Solarix\n - 12T FT-ICR MS\n - 12T MRMS\n solarix_15T:\n text: solarix_15T\n aliases:\n - 15T Solarix\n - 15T FT-ICR MS\n - 15T MRMS\n agilent_8890A:\n text: agilent_8890A\n aliases:\n - 8890A GC-MS\n - Agilent GC MS\n agilent_7980A:\n text: agilent_7980A\n aliases:\n - 7980A GC-MS\n - Agilent GC MS\n vortex_genie_2:\n text: vortex_genie_2\n aliases:\n - VortexGenie2\n novaseq:\n text: novaseq\n aliases:\n - NovaSeq\n - Illumina NovaSeq\n novaseq_6000:\n text: novaseq_6000\n meaning: OBI:0002630\n comments:\n - Possible flowcell versions are SP, S1, S2, S4.\n see_also:\n - https://www.illumina.com/systems/sequencing-platforms/novaseq/specifications.html\n aliases:\n - NovaSeq 6000\n - Illumina NovaSeq 6000\n structured_aliases:\n Illumina NovaSeq S2:\n literal_form: Illumina NovaSeq S2\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n Illumina NovaSeq S4:\n literal_form: Illumina NovaSeq S4\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n Illumina NovaSeq SP:\n literal_form: Illumina NovaSeq SP\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n novaseq_x:\n text: novaseq_x\n comments:\n - Possible flowcell versions are 1.5B, 10B, 25B. Only difference between X and\n X Plus is 2 flowcells for X Plus versus 1 flowcell for X.\n see_also:\n - https://www.illumina.com/systems/sequencing-platforms/novaseq-x-plus/specifications.html\n aliases:\n - Illumina NovaSeq X\n - Illumina NovaSeq X Plus\n hiseq:\n text: hiseq\n aliases:\n - Illumina HiSeq\n hiseq_1000:\n text: hiseq_1000\n meaning: OBI:0002022\n aliases:\n - Illumina HiSeq 1000\n hiseq_1500:\n text: hiseq_1500\n meaning: OBI:0003386\n aliases:\n - Illumina HiSeq 1500\n hiseq_2000:\n text: hiseq_2000\n meaning: OBI:0002001\n aliases:\n - Illumina HiSeq 2000\n hiseq_2500:\n text: hiseq_2500\n meaning: OBI:0002002\n aliases:\n - Illumina HiSeq 2500\n structured_aliases:\n Illumina HiSeq 2500-1TB:\n literal_form: Illumina HiSeq 2500-1TB\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n Illumina HiSeq 2500-Rapid:\n literal_form: Illumina HiSeq 2500-Rapid\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n hiseq_3000:\n text: hiseq_3000\n meaning: OBI:0002048\n aliases:\n - Illumina HiSeq 3000\n hiseq_4000:\n text: hiseq_4000\n meaning: OBI:0002049\n aliases:\n - Illumina HiSeq 4000\n hiseq_x_ten:\n text: hiseq_x_ten\n meaning: OBI:0002129\n aliases:\n - Illumina HiSeq X Ten\n miniseq:\n text: miniseq\n meaning: OBI:0003114\n aliases:\n - Illumina MiniSeq\n miseq:\n text: miseq\n meaning: OBI:0002003\n aliases:\n - MiSeq\n - Illumina MiSeq\n nextseq_1000:\n text: nextseq_1000\n meaning: OBI:0003606\n aliases:\n - Illumina NextSeq 1000\n nextseq:\n text: nextseq\n aliases:\n - NextSeq\n - Illumina NextSeq\n structured_aliases:\n Illumina NextSeq-HO:\n literal_form: Illumina NextSeq-HO\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n Illumina NextSeq-MO:\n literal_form: Illumina NextSeq-MO\n predicate: NARROW_SYNONYM\n contexts:\n - https://gold.jgi.doe.gov/\n nextseq_500:\n text: nextseq_500\n meaning: OBI:0002021\n aliases:\n - NextSeq 500\n - Illumina NextSeq 500\n nextseq_550:\n text: nextseq_550\n meaning: OBI:0003387\n aliases:\n - NextSeq 550\n - Illumina NextSeq 550\n gridion:\n text: gridion\n meaning: OBI:0002751\n aliases:\n - Oxford Nanopore GridION Mk1\n minion:\n text: minion\n meaning: OBI:0002750\n aliases:\n - Oxford Nanopore MinION\n promethion:\n text: promethion\n meaning: OBI:0002752\n aliases:\n - Oxford Nanopore PromethION\n rs_II:\n text: rs_II\n meaning: OBI:0002012\n aliases:\n - PacBio RS II\n sequel:\n text: sequel\n meaning: OBI:0002632\n aliases:\n - PacBio Sequel\n sequel_II:\n text: sequel_II\n meaning: OBI:0002633\n aliases:\n - PacBio Sequel II\n revio:\n text: revio\n aliases:\n - PacBio Revio\n - Revio\n\nURI: InstrumentVendorEnum
"},{"location":"InstrumentVendorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description waters None agilent None bruker None thermo_fisher None vwr None perkin_elmer None gilson None scientific_industries None illumina OBI:0000759 pacbio OBI:0001856 oxford_nanopore OBI:0002755 pnnl None"},{"location":"InstrumentVendorEnum/#slots","title":"Slots","text":"Name Description vendor"},{"location":"InstrumentVendorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"InstrumentVendorEnum/#schema-source","title":"Schema Source","text":"name: InstrumentVendorEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n waters:\n text: waters\n aliases:\n - Waters Corporation\n agilent:\n text: agilent\n aliases:\n - Agilent Technologies\n bruker:\n text: bruker\n aliases:\n - Bruker Corporation\n - Bruker Daltonics\n thermo_fisher:\n text: thermo_fisher\n aliases:\n - ThermoFisher\n - Thermo Fisher Scientific\n vwr:\n text: vwr\n perkin_elmer:\n text: perkin_elmer\n gilson:\n text: gilson\n scientific_industries:\n text: scientific_industries\n illumina:\n text: illumina\n meaning: OBI:0000759\n aliases:\n - Illumina\n pacbio:\n text: pacbio\n meaning: OBI:0001856\n aliases:\n - PacBio\n - Pacific Biosciences\n oxford_nanopore:\n text: oxford_nanopore\n meaning: OBI:0002755\n aliases:\n - Oxford Nanopore Technologies\n pnnl:\n text: pnnl\n aliases:\n - PNNL\n\nURI: IntWallCondEnum
"},{"location":"IntWallCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None"},{"location":"IntWallCondEnum/#slots","title":"Slots","text":"Name Description int_wall_cond The physical condition of the wall at the time of sampling; photos or video p..."},{"location":"IntWallCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IntWallCondEnum/#schema-source","title":"Schema Source","text":"name: int_wall_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n\nAn integer
URI: xsd:integer
base: int
uri: xsd:integer
URI: IonizationSourceEnum
"},{"location":"IonizationSourceEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description electrospray_ionization None matrix_assisted_laser_desorption_ionization None atmospheric_pressure_photo_ionization None atmospheric_pressure_chemical_ionization None electron_ionization None"},{"location":"IonizationSourceEnum/#slots","title":"Slots","text":"Name Description ionization_source The ionization source used to introduce processed samples into a mass spectro..."},{"location":"IonizationSourceEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"IonizationSourceEnum/#schema-source","title":"Schema Source","text":"name: IonizationSourceEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n electrospray_ionization:\n text: electrospray_ionization\n aliases:\n - ESI\n matrix_assisted_laser_desorption_ionization:\n text: matrix_assisted_laser_desorption_ionization\n aliases:\n - MALDI\n atmospheric_pressure_photo_ionization:\n text: atmospheric_pressure_photo_ionization\n aliases:\n - APPI\n atmospheric_pressure_chemical_ionization:\n text: atmospheric_pressure_chemical_ionization\n aliases:\n - APCI\n electron_ionization:\n text: electron_ionization\n aliases:\n - EI\n\nURI: JgiContTypeEnum
"},{"location":"JgiContTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plate None tube None"},{"location":"JgiContTypeEnum/#slots","title":"Slots","text":"Name Description dna_cont_type Tube or plate (96-well) rna_cont_type Tube or plate (96-well)"},{"location":"JgiContTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"JgiContTypeEnum/#schema-source","title":"Schema Source","text":"name: JgiContTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n plate:\n text: plate\n tube:\n text: tube\n\nA string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A language code conforming to ISO_639-1
URI: xsd:language
base: str
uri: xsd:language
URI: nmdc:LibraryPreparation
classDiagram\n class LibraryPreparation\n click LibraryPreparation href \"../LibraryPreparation\"\n MaterialProcessing <|-- LibraryPreparation\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n LibraryPreparation : alternative_identifiers\n\n LibraryPreparation : description\n\n LibraryPreparation : end_date\n\n LibraryPreparation : has_failure_categorization\n\n LibraryPreparation --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n LibraryPreparation : has_input\n\n LibraryPreparation --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n LibraryPreparation : has_output\n\n LibraryPreparation --> \"1..*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n LibraryPreparation : id\n\n LibraryPreparation : instrument_used\n\n LibraryPreparation --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n LibraryPreparation : is_stranded\n\n LibraryPreparation : library_preparation_kit\n\n LibraryPreparation : library_type\n\n LibraryPreparation --> \"0..1\" LibraryTypeEnum : library_type\n click LibraryTypeEnum href \"../LibraryTypeEnum\"\n\n LibraryPreparation : name\n\n LibraryPreparation : nucl_acid_amp\n\n LibraryPreparation --> \"0..1\" TextValue : nucl_acid_amp\n click TextValue href \"../TextValue\"\n\n LibraryPreparation : pcr_cond\n\n LibraryPreparation --> \"0..1\" TextValue : pcr_cond\n click TextValue href \"../TextValue\"\n\n LibraryPreparation : pcr_cycles\n\n LibraryPreparation : pcr_primers\n\n LibraryPreparation --> \"0..1\" TextValue : pcr_primers\n click TextValue href \"../TextValue\"\n\n LibraryPreparation : processing_institution\n\n LibraryPreparation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n LibraryPreparation : protocol_link\n\n LibraryPreparation --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n LibraryPreparation : qc_comment\n\n LibraryPreparation : qc_status\n\n LibraryPreparation --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n LibraryPreparation : start_date\n\n LibraryPreparation : stranded_orientation\n\n LibraryPreparation --> \"0..1\" StrandedOrientationEnum : stranded_orientation\n click StrandedOrientationEnum href \"../StrandedOrientationEnum\"\n\n LibraryPreparation : type\n\n\n\nname: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: MaterialProcessing\nslots:\n- is_stranded\n- library_preparation_kit\n- library_type\n- nucl_acid_amp\n- pcr_cond\n- pcr_cycles\n- pcr_primers\n- stranded_orientation\nslot_usage:\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n interpolated: true\n pcr_cond:\n name: pcr_cond\n description: Description of reaction conditions and components of polymerase chain\n reaction performed during library preparation\nclass_uri: nmdc:LibraryPreparation\n\nname: LibraryPreparation\ncomments:\n- OBI:0000711 specifies a DNA input (but not ONLY a DNA input)\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- LibraryConstruction\nclose_mappings:\n- OBI:0000711\nis_a: MaterialProcessing\nslot_usage:\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n interpolated: true\n pcr_cond:\n name: pcr_cond\n description: Description of reaction conditions and components of polymerase chain\n reaction performed during library preparation\nattributes:\n is_stranded:\n name: is_stranded\n description: Is the (RNA) library stranded or non-stranded (unstranded).\n comments:\n - A value of true means the library is stranded, flase means non-stranded.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: is_stranded\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: boolean\n library_preparation_kit:\n name: library_preparation_kit\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: library_preparation_kit\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: string\n library_type:\n name: library_type\n title: library type\n examples:\n - value: DNA\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: library_type\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: LibraryTypeEnum\n nucl_acid_amp:\n name: nucl_acid_amp\n annotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\n description: A link to a literature reference, electronic resource or a standard\n operating procedure (SOP), that describes the enzymatic amplification (PCR,\n TMA, NASBA) of specific nucleic acids\n title: nucleic acid amplification\n examples:\n - value: https://phylogenomics.me/protocols/16s-pcr-protocol/\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - nucleic acid amplification\n rank: 1000\n is_a: sequencing field\n string_serialization: '{PMID}|{DOI}|{URL}'\n slot_uri: MIXS:0000038\n alias: nucl_acid_amp\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: TextValue\n multivalued: false\n pcr_cond:\n name: pcr_cond\n annotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n description: Description of reaction conditions and components of polymerase chain\n reaction performed during library preparation\n title: pcr conditions\n examples:\n - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr conditions\n rank: 1000\n is_a: sequencing field\n string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\n slot_uri: MIXS:0000049\n alias: pcr_cond\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: TextValue\n multivalued: false\n pcr_cycles:\n name: pcr_cycles\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - OBI:0002475\n rank: 1000\n alias: pcr_cycles\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: integer\n pcr_primers:\n name: pcr_primers\n annotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\n description: PCR primers that were used to amplify the sequence of the targeted\n gene, locus or subfragment. This field should contain all the primers used for\n a single PCR reaction if multiple forward or reverse primers are present in\n a single PCR reaction. The primer sequence should be reported in uppercase letters\n title: pcr primers\n examples:\n - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - pcr primers\n rank: 1000\n is_a: sequencing field\n string_serialization: FWD:{dna};REV:{dna}\n slot_uri: MIXS:0000046\n alias: pcr_primers\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: TextValue\n multivalued: false\n stranded_orientation:\n name: stranded_orientation\n description: Lists the strand orientiation for a stranded RNA library preparation.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: stranded_orientation\n owner: LibraryPreparation\n domain_of:\n - LibraryPreparation\n range: StrandedOrientationEnum\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: LibraryPreparation\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: LibraryPreparation\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: LibraryPreparation\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:libprp-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: LibraryPreparation\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: LibraryPreparation\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: LibraryPreparation\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: LibraryPreparation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:LibraryPreparation\n\nURI: LibraryTypeEnum
"},{"location":"LibraryTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DNA None RNA None"},{"location":"LibraryTypeEnum/#slots","title":"Slots","text":"Name Description library_type"},{"location":"LibraryTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LibraryTypeEnum/#schema-source","title":"Schema Source","text":"name: LibraryTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DNA:\n text: DNA\n RNA:\n text: RNA\n\nURI: LightTypeEnum
"},{"location":"LightTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description natural light None electric light None desk lamp None flourescent lights None none None"},{"location":"LightTypeEnum/#slots","title":"Slots","text":"Name Description light_type Application of light to achieve some practical or aesthetic effect"},{"location":"LightTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LightTypeEnum/#schema-source","title":"Schema Source","text":"name: light_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n natural light:\n text: natural light\n electric light:\n text: electric light\n desk lamp:\n text: desk lamp\n flourescent lights:\n text: flourescent lights\n none:\n text: none\n\nURI: LithologyEnum
"},{"location":"LithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Basement None Chalk None Chert None Coal None Conglomerate None Diatomite None Dolomite None Limestone None Sandstone None Shale None Siltstone None Volcanic None other None"},{"location":"LithologyEnum/#slots","title":"Slots","text":"Name Description lithology Hydrocarbon resource main lithology (Additional information: http://petrowiki"},{"location":"LithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"LithologyEnum/#schema-source","title":"Schema Source","text":"name: lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Basement:\n text: Basement\n Chalk:\n text: Chalk\n Chert:\n text: Chert\n Coal:\n text: Coal\n Conglomerate:\n text: Conglomerate\n Diatomite:\n text: Diatomite\n Dolomite:\n text: Dolomite\n Limestone:\n text: Limestone\n Sandstone:\n text: Sandstone\n Shale:\n text: Shale\n Siltstone:\n text: Siltstone\n Volcanic:\n text: Volcanic\n other:\n text: other\n\nURI: nmdc:MagBin
classDiagram\n class MagBin\n click MagBin href \"../MagBin\"\n\n MagBin : bin_name\n\n MagBin : bin_quality\n\n MagBin --> \"0..1\" BinQualityEnum : bin_quality\n click BinQualityEnum href \"../BinQualityEnum\"\n\n MagBin : completeness\n\n MagBin : contamination\n\n MagBin : eukaryotic_evaluation\n\n MagBin --> \"0..1\" EukEval : eukaryotic_evaluation\n click EukEval href \"../EukEval\"\n\n MagBin : gene_count\n\n MagBin : gtdbtk_class\n\n MagBin : gtdbtk_domain\n\n MagBin : gtdbtk_family\n\n MagBin : gtdbtk_genus\n\n MagBin : gtdbtk_order\n\n MagBin : gtdbtk_phylum\n\n MagBin : gtdbtk_species\n\n MagBin : members_id\n\n MagBin : num_16s\n\n MagBin : num_23s\n\n MagBin : num_5s\n\n MagBin : num_t_rna\n\n MagBin : number_of_contig\n\n MagBin : total_bases\n\n MagBin : type\n\n\n\nname: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- bin_name\n- bin_quality\n- completeness\n- contamination\n- gene_count\n- gtdbtk_class\n- gtdbtk_domain\n- gtdbtk_family\n- gtdbtk_genus\n- gtdbtk_order\n- gtdbtk_phylum\n- gtdbtk_species\n- members_id\n- num_16s\n- num_23s\n- num_5s\n- num_t_rna\n- number_of_contig\n- total_bases\n- type\n- eukaryotic_evaluation\nclass_uri: nmdc:MagBin\n\nname: MagBin\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n bin_name:\n name: bin_name\n description: Name of the metagenome-assembled genome.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bin_name\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n required: true\n bin_quality:\n name: bin_quality\n description: The quality of the metagenome-assembled genome based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: bin_quality\n owner: MagBin\n domain_of:\n - MagBin\n range: BinQualityEnum\n completeness:\n name: completeness\n description: Estimate of the completeness of the metagenome-assembled genome,\n estimated by a tool like CheckM.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: completeness\n owner: MagBin\n domain_of:\n - EukEval\n - MagBin\n range: float\n minimum_value: 0\n contamination:\n name: contamination\n description: Estimate of the completeness of the metagenome-assembled genome,\n estimated by a tool like CheckM.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contamination\n owner: MagBin\n domain_of:\n - EukEval\n - MagBin\n range: float\n minimum_value: 0\n gene_count:\n name: gene_count\n description: Number of genes.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: gene_count\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n gtdbtk_class:\n name: gtdbtk_class\n description: Taxonomic class assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:class\n rank: 1000\n alias: gtdbtk_class\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_domain:\n name: gtdbtk_domain\n description: Taxonomic domain assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:superkingdom\n rank: 1000\n alias: gtdbtk_domain\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_family:\n name: gtdbtk_family\n description: Taxonomic family assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:family\n rank: 1000\n alias: gtdbtk_family\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_genus:\n name: gtdbtk_genus\n description: Taxonomic genus assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:genus\n rank: 1000\n alias: gtdbtk_genus\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_order:\n name: gtdbtk_order\n description: Taxonomic order assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:order\n rank: 1000\n alias: gtdbtk_order\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_phylum:\n name: gtdbtk_phylum\n description: Taxonomic phylum assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:phylum\n rank: 1000\n alias: gtdbtk_phylum\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n gtdbtk_species:\n name: gtdbtk_species\n description: Taxonomic genus assigned by GTDB-Tk.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://doi.org/10.1093/bioinformatics/btz848\n exact_mappings:\n - NCBITaxon:species\n rank: 1000\n alias: gtdbtk_species\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n members_id:\n name: members_id\n description: Names of the contigs that make up a metagenome-assembled genome.\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - GENEPIO:0100596\n rank: 1000\n alias: members_id\n owner: MagBin\n domain_of:\n - MagBin\n range: string\n multivalued: true\n num_16s:\n name: num_16s\n description: Number of 16s sequences detected, a subunit of prokaryotic ribosomes.\n from_schema: https://w3id.org/nmdc/nmdc\n broad_mappings:\n - NCIT:C105370\n rank: 1000\n alias: num_16s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n num_23s:\n name: num_23s\n description: Number of 23 seqeuences detected, a subunit of ribosomes.\n from_schema: https://w3id.org/nmdc/nmdc\n broad_mappings:\n - OMIT:0013245\n rank: 1000\n alias: num_23s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n num_5s:\n name: num_5s\n description: Number of 5s seqeuences detected, a subunit of ribosomes.\n from_schema: https://w3id.org/nmdc/nmdc\n broad_mappings:\n - OMIT:0013248\n rank: 1000\n alias: num_5s\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n num_t_rna:\n name: num_t_rna\n description: Number of transfer transfer RNAs.\n from_schema: https://w3id.org/nmdc/nmdc\n broad_mappings:\n - NCIT:C816\n rank: 1000\n alias: num_t_rna\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n number_of_contig:\n name: number_of_contig\n description: Number of contigs\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - GENEPIO:0000093\n rank: 1000\n alias: number_of_contig\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n total_bases:\n name: total_bases\n description: Total number of basepairs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: total_bases\n owner: MagBin\n domain_of:\n - MagBin\n range: integer\n minimum_value: 0\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MagBin\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n eukaryotic_evaluation:\n name: eukaryotic_evaluation\n description: Contains results from evaluating if a Metagenome-Assembled Genome\n is of eukaryotic lineage.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: eukaryotic_evaluation\n owner: MagBin\n domain_of:\n - MagBin\n range: EukEval\nclass_uri: nmdc:MagBin\n\nA workflow execution activity that uses computational binning tools to group assembled contigs into genomes
URI: nmdc:MagsAnalysis
classDiagram\n class MagsAnalysis\n click MagsAnalysis href \"../MagsAnalysis\"\n WorkflowExecution <|-- MagsAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MagsAnalysis : alternative_identifiers\n\n MagsAnalysis : binned_contig_num\n\n MagsAnalysis : description\n\n MagsAnalysis : end_date\n\n MagsAnalysis : ended_at_time\n\n MagsAnalysis : execution_resource\n\n MagsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MagsAnalysis : git_url\n\n MagsAnalysis : has_failure_categorization\n\n MagsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MagsAnalysis : has_input\n\n MagsAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MagsAnalysis : has_output\n\n MagsAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MagsAnalysis : id\n\n MagsAnalysis : img_identifiers\n\n MagsAnalysis : input_contig_num\n\n MagsAnalysis : low_depth_contig_num\n\n MagsAnalysis : mags_list\n\n MagsAnalysis --> \"*\" MagBin : mags_list\n click MagBin href \"../MagBin\"\n\n MagsAnalysis : name\n\n MagsAnalysis : processing_institution\n\n MagsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MagsAnalysis : protocol_link\n\n MagsAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MagsAnalysis : qc_comment\n\n MagsAnalysis : qc_status\n\n MagsAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MagsAnalysis : start_date\n\n MagsAnalysis : started_at_time\n\n MagsAnalysis : too_short_contig_num\n\n MagsAnalysis : type\n\n MagsAnalysis : unbinned_contig_num\n\n MagsAnalysis : version\n\n MagsAnalysis : was_informed_by\n\n MagsAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MagsAnalysis\ndescription: A workflow execution activity that uses computational binning tools to\n group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- binned_contig_num\n- input_contig_num\n- low_depth_contig_num\n- mags_list\n- too_short_contig_num\n- unbinned_contig_num\n- img_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MagsAnalysis\n\nname: MagsAnalysis\ndescription: A workflow execution activity that uses computational binning tools to\n group assembled contigs into genomes\ntitle: Metagenome-Assembled Genome analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n binned_contig_num:\n name: binned_contig_num\n description: Number of contigs that ended up in a medium or high quality bin.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: binned_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n input_contig_num:\n name: input_contig_num\n description: Total number of input contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: input_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n low_depth_contig_num:\n name: low_depth_contig_num\n description: Number of contigs which were excluded from binning for depth of coverage.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: low_depth_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n mags_list:\n name: mags_list\n description: Contains detailed information about each metagenome-assembled genome.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mags_list\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: MagBin\n multivalued: true\n inlined: true\n inlined_as_list: true\n too_short_contig_num:\n name: too_short_contig_num\n description: Number of contigs which were excluded from binning for length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: too_short_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n unbinned_contig_num:\n name: unbinned_contig_num\n description: Number of contigs which did not end up in a medium or high quality\n bin.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: unbinned_contig_num\n owner: MagsAnalysis\n domain_of:\n - MagsAnalysis\n range: integer\n minimum_value: 0\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: MagsAnalysis\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n maximum_cardinality: 1\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MagsAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MagsAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MagsAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmag-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MagsAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MagsAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MagsAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MagsAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MagsAnalysis\n\nA qualified collection of DataObjects that can be analyzed together in the same experimental context.
URI: nmdc:Manifest
classDiagram\n class Manifest\n click Manifest href \"../Manifest\"\n InformationObject <|-- Manifest\n click InformationObject href \"../InformationObject\"\n\n\n\n Manifest : alternative_identifiers\n\n Manifest : description\n\n Manifest : id\n\n Manifest : manifest_category\n\n Manifest --> \"1\" ManifestCategoryEnum : manifest_category\n click ManifestCategoryEnum href \"../ManifestCategoryEnum\"\n\n Manifest : name\n\n Manifest : type\n\n\n\nname: Manifest\ndescription: A qualified collection of DataObjects that can be analyzed together in\n the same experimental context.\ncomments:\n- Manifest are currently uncoupled from other modelling. For example, there is no\n schema requirement that DataObjects in a fractions Manifest were all obtained by\n analyzing the same ProcessedSample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslots:\n- manifest_category\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\nclass_uri: nmdc:Manifest\n\nname: Manifest\ndescription: A qualified collection of DataObjects that can be analyzed together in\n the same experimental context.\ncomments:\n- Manifest are currently uncoupled from other modelling. For example, there is no\n schema requirement that DataObjects in a fractions Manifest were all obtained by\n analyzing the same ProcessedSample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: InformationObject\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\nattributes:\n manifest_category:\n name: manifest_category\n description: The type of context in which the constituent DataObjects can be analyzed\n together.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: manifest_category\n owner: Manifest\n domain_of:\n - Manifest\n range: ManifestCategoryEnum\n required: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Manifest\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$'\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Manifest\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Manifest\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Manifest\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Manifest\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Manifest\n\nA list of contexts in which some DataObjects can be analyzed together.
URI: ManifestCategoryEnum
"},{"location":"ManifestCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description instrument_run None A collection of data objects from a single run of an instrument poolable_replicates None A collection of data objects that can be pooled for downstream analyses fractions None A collection of data objects that represent fractions of a single sample"},{"location":"ManifestCategoryEnum/#slots","title":"Slots","text":"Name Description manifest_category The type of context in which the constituent DataObjects can be analyzed toge..."},{"location":"ManifestCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ManifestCategoryEnum/#schema-source","title":"Schema Source","text":"name: ManifestCategoryEnum\ndescription: A list of contexts in which some DataObjects can be analyzed together.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n instrument_run:\n text: instrument_run\n description: A collection of data objects from a single run of an instrument.\n poolable_replicates:\n text: poolable_replicates\n description: A collection of data objects that can be pooled for downstream analyses.\n fractions:\n text: fractions\n description: A collection of data objects that represent fractions of a single\n sample.\n\nURI: MassAnalyzerEnum
"},{"location":"MassAnalyzerEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description time_of_flight None Instrument that separates ions by m/z in a field-free region after accelerati... quadrupole None A mass spectrometer that consists of four parallel rods whose centers form th... Orbitrap None An ion trapping device that consists of an outer barrel-like electrode and a ... ion_cyclotron_resonance None A mass spectrometer based on the principle of ion cyclotron resonance in whic... ion_trap None A device for spatially confining ions using electric and magnetic fields alon..."},{"location":"MassAnalyzerEnum/#slots","title":"Slots","text":"Name Description mass_analyzers The kind of mass analyzer(s) used during the spectra collection"},{"location":"MassAnalyzerEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassAnalyzerEnum/#schema-source","title":"Schema Source","text":"name: MassAnalyzerEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n time_of_flight:\n text: time_of_flight\n description: Instrument that separates ions by m/z in a field-free region after\n acceleration to a fixed acceleration energy.\n aliases:\n - TOF\n exact_mappings:\n - MS:1000084\n quadrupole:\n text: quadrupole\n description: A mass spectrometer that consists of four parallel rods whose centers\n form the corners of a square and whose opposing poles are connected. The voltage\n applied to the rods is a superposition of a static potential and a sinusoidal\n radio frequency potential. The motion of an ion in the x and y dimensions is\n described by the Matthieu equation whose solutions show that ions in a particular\n m/z range can be transmitted along the z axis.\n aliases:\n - Quad\n - Q\n exact_mappings:\n - MS:1000081\n Orbitrap:\n text: Orbitrap\n description: An ion trapping device that consists of an outer barrel-like electrode\n and a coaxial inner spindle-like electrode that form an electrostatic field\n with quadro-logarithmic potential distribution. The frequency of harmonic oscillations\n of the orbitally trapped ions along the axis of the electrostatic field is independent\n of the ion velocity and is inversely proportional to the square root of m/z\n so that the trap can be used as a mass analyzer.\n aliases:\n - Orbi\n exact_mappings:\n - MS:1000484\n ion_cyclotron_resonance:\n text: ion_cyclotron_resonance\n description: A mass spectrometer based on the principle of ion cyclotron resonance\n in which an ion in a magnetic field moves in a circular orbit at a frequency\n characteristic of its m/z value. Ions are coherently excited to a larger radius\n orbit using a pulse of radio frequency energy and their image charge is detected\n on receiver plates as a time domain signal. Fourier transformation of the time\n domain signal results in a frequency domain signal which is converted to a mass\n spectrum based in the inverse relationship between frequency and m/z.\n aliases:\n - ICR\n exact_mappings:\n - MS:1000079\n ion_trap:\n text: ion_trap\n description: A device for spatially confining ions using electric and magnetic\n fields alone or in combination.\n aliases:\n - LTQ\n - Ion Trap\n - Paul Trap\n exact_mappings:\n - MS:1000264\n\nSpectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.
URI: nmdc:MassSpectrometry
classDiagram\n class MassSpectrometry\n click MassSpectrometry href \"../MassSpectrometry\"\n DataGeneration <|-- MassSpectrometry\n click DataGeneration href \"../DataGeneration\"\n\n\n\n MassSpectrometry : add_date\n\n MassSpectrometry : alternative_identifiers\n\n MassSpectrometry : analyte_category\n\n MassSpectrometry --> \"1\" MassSpectrometryEnum : analyte_category\n click MassSpectrometryEnum href \"../MassSpectrometryEnum\"\n\n MassSpectrometry : associated_studies\n\n MassSpectrometry --> \"1..*\" Study : associated_studies\n click Study href \"../Study\"\n\n MassSpectrometry : description\n\n MassSpectrometry : eluent_introduction_category\n\n MassSpectrometry --> \"0..1\" EluentIntroductionCategoryEnum : eluent_introduction_category\n click EluentIntroductionCategoryEnum href \"../EluentIntroductionCategoryEnum\"\n\n MassSpectrometry : end_date\n\n MassSpectrometry : generates_calibration\n\n MassSpectrometry --> \"0..1\" CalibrationInformation : generates_calibration\n click CalibrationInformation href \"../CalibrationInformation\"\n\n MassSpectrometry : has_chromatography_configuration\n\n MassSpectrometry --> \"0..1\" ChromatographyConfiguration : has_chromatography_configuration\n click ChromatographyConfiguration href \"../ChromatographyConfiguration\"\n\n MassSpectrometry : has_failure_categorization\n\n MassSpectrometry --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MassSpectrometry : has_input\n\n MassSpectrometry --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n MassSpectrometry : has_mass_spectrometry_configuration\n\n MassSpectrometry --> \"0..1\" MassSpectrometryConfiguration : has_mass_spectrometry_configuration\n click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n\n MassSpectrometry : has_output\n\n MassSpectrometry --> \"*\" DataObject : has_output\n click DataObject href \"../DataObject\"\n\n MassSpectrometry : id\n\n MassSpectrometry : instrument_used\n\n MassSpectrometry --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n MassSpectrometry : mod_date\n\n MassSpectrometry : name\n\n MassSpectrometry : principal_investigator\n\n MassSpectrometry --> \"0..1\" PersonValue : principal_investigator\n click PersonValue href \"../PersonValue\"\n\n MassSpectrometry : processing_institution\n\n MassSpectrometry --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MassSpectrometry : protocol_link\n\n MassSpectrometry --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MassSpectrometry : qc_comment\n\n MassSpectrometry : qc_status\n\n MassSpectrometry --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MassSpectrometry : start_date\n\n MassSpectrometry : type\n\n\n\nname: MassSpectrometry\ndescription: Spectrometry where the sample is converted into gaseous ions which are\n characterised by their mass-to-charge ratio and relative abundance.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- CHMO:0000470\nis_a: DataGeneration\nslots:\n- eluent_introduction_category\n- generates_calibration\n- has_chromatography_configuration\n- has_mass_spectrometry_configuration\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_chromatography_configuration:\n name: has_chromatography_configuration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_mass_spectrometry_configuration:\n name: has_mass_spectrometry_configuration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\n analyte_category:\n name: analyte_category\n range: MassSpectrometryEnum\nclass_uri: nmdc:MassSpectrometry\nrules:\n- preconditions:\n slot_conditions:\n eluent_introduction_category:\n name: eluent_introduction_category\n equals_string: gas_chromatography\n postconditions:\n slot_conditions:\n generates_calibration:\n name: generates_calibration\n required: true\n description: If eluent_introduction_category is gas_chromatography, then generates_calibration\n is required.\n title: generates_calibration_required_if_gc\n- preconditions:\n slot_conditions:\n eluent_introduction_category:\n name: eluent_introduction_category\n any_of:\n - equals_string: liquid_chromatography\n - equals_string: gas_chromatography\n postconditions:\n slot_conditions:\n has_chromatography_configuration:\n name: has_chromatography_configuration\n required: true\n description: If eluent_introduction_category is liquid_chromatography or gas_chromatography,\n then has_chromatography_configuration is required.\n title: has_chromatography_configuration_required_if_lc_or_gc\n\nname: MassSpectrometry\ndescription: Spectrometry where the sample is converted into gaseous ions which are\n characterised by their mass-to-charge ratio and relative abundance.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- CHMO:0000470\nis_a: DataGeneration\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_chromatography_configuration:\n name: has_chromatography_configuration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_mass_spectrometry_configuration:\n name: has_mass_spectrometry_configuration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\n analyte_category:\n name: analyte_category\n range: MassSpectrometryEnum\nattributes:\n eluent_introduction_category:\n name: eluent_introduction_category\n description: A high-level categorization for how the processed sample is introduced\n into a mass spectrometer.\n examples:\n - value: liquid_chromatography\n - value: direct_infusion_syringe\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: eluent_introduction_category\n owner: MassSpectrometry\n domain_of:\n - MassSpectrometry\n range: EluentIntroductionCategoryEnum\n generates_calibration:\n name: generates_calibration\n description: calibration information is generated a process\n comments:\n - A gas chromatography mass spectromery run generates data to calibrate the retention\n index\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: generates_calibration\n owner: MassSpectrometry\n domain_of:\n - MassSpectrometry\n range: CalibrationInformation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_chromatography_configuration:\n name: has_chromatography_configuration\n description: The identifier of the associated ChromatographyConfiguration, providing\n information about how a sample was introduced into the mass spectrometer.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_chromatography_configuration\n owner: MassSpectrometry\n domain_of:\n - MassSpectrometry\n range: ChromatographyConfiguration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:chrcon-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_mass_spectrometry_configuration:\n name: has_mass_spectrometry_configuration\n description: The identifier of the associated MassSpectrometryConfiguration.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_mass_spectrometry_configuration\n owner: MassSpectrometry\n domain_of:\n - MassSpectrometry\n range: MassSpectrometryConfiguration\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: MassSpectrometry\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n analyte_category:\n name: analyte_category\n description: \"The type of analyte(s) that were measured in the data generation\\\n \\ process and analyzed\\n in the Workflow Chain\\n\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: analyte_category\n owner: MassSpectrometry\n domain_of:\n - DataGeneration\n range: MassSpectrometryEnum\n required: true\n associated_studies:\n name: associated_studies\n description: The study associated with a resource.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: associated_studies\n owner: MassSpectrometry\n domain_of:\n - Biosample\n - DataGeneration\n range: Study\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: MassSpectrometry\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: MassSpectrometry\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n alias: principal_investigator\n owner: MassSpectrometry\n domain_of:\n - Study\n - DataGeneration\n range: PersonValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: DataObject\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MassSpectrometry\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MassSpectrometry\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgms|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MassSpectrometry\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MassSpectrometry\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MassSpectrometry\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MassSpectrometry\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MassSpectrometry\nrules:\n- preconditions:\n slot_conditions:\n eluent_introduction_category:\n name: eluent_introduction_category\n equals_string: gas_chromatography\n postconditions:\n slot_conditions:\n generates_calibration:\n name: generates_calibration\n required: true\n description: If eluent_introduction_category is gas_chromatography, then generates_calibration\n is required.\n title: generates_calibration_required_if_gc\n- preconditions:\n slot_conditions:\n eluent_introduction_category:\n name: eluent_introduction_category\n any_of:\n - equals_string: liquid_chromatography\n - equals_string: gas_chromatography\n postconditions:\n slot_conditions:\n has_chromatography_configuration:\n name: has_chromatography_configuration\n required: true\n description: If eluent_introduction_category is liquid_chromatography or gas_chromatography,\n then has_chromatography_configuration is required.\n title: has_chromatography_configuration_required_if_lc_or_gc\n\nURI: MassSpectrometryAcquisitionStrategyEnum
"},{"location":"MassSpectrometryAcquisitionStrategyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description data_independent_acquisition None ['Data independent mass spectrometer acquisition method wherein the full mass... data_dependent_acquisition None Mass spectrometer data acquisition method wherein MSn spectra are triggered b... full_scan_only None Mass spectrometer data acquisition method wherein only MS1 data are acquired"},{"location":"MassSpectrometryAcquisitionStrategyEnum/#slots","title":"Slots","text":"Name Description mass_spectrometry_acquisition_strategy Mode of running a mass spectrometer method by which m/z ranges are selected a..."},{"location":"MassSpectrometryAcquisitionStrategyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometryAcquisitionStrategyEnum/#schema-source","title":"Schema Source","text":"name: MassSpectrometryAcquisitionStrategyEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n data_independent_acquisition:\n text: data_independent_acquisition\n description: '[''Data independent mass spectrometer acquisition method wherein\n the full mass range is fragmented. Examples of such an approach include MS^E,\n AIF, and bbCID.'']'\n aliases:\n - DIA\n - data independent acquisition from dissociation of full mass range\n exact_mappings:\n - MS:1003227\n data_dependent_acquisition:\n text: data_dependent_acquisition\n description: Mass spectrometer data acquisition method wherein MSn spectra are\n triggered based on the m/z of precursor ions detected in the same run.\n aliases:\n - -DDA\n exact_mappings:\n - MS:1003221\n full_scan_only:\n text: full_scan_only\n description: Mass spectrometer data acquisition method wherein only MS1 data are\n acquired.\n aliases:\n - MS\n\nA set of parameters that define and control the actions of a mass spectrometry process.
URI: nmdc:MassSpectrometryConfiguration
classDiagram\n class MassSpectrometryConfiguration\n click MassSpectrometryConfiguration href \"../MassSpectrometryConfiguration\"\n Configuration <|-- MassSpectrometryConfiguration\n click Configuration href \"../Configuration\"\n\n\n\n MassSpectrometryConfiguration : alternative_identifiers\n\n MassSpectrometryConfiguration : description\n\n MassSpectrometryConfiguration : id\n\n MassSpectrometryConfiguration : ionization_source\n\n MassSpectrometryConfiguration --> \"0..1\" IonizationSourceEnum : ionization_source\n click IonizationSourceEnum href \"../IonizationSourceEnum\"\n\n MassSpectrometryConfiguration : mass_analyzers\n\n MassSpectrometryConfiguration --> \"*\" MassAnalyzerEnum : mass_analyzers\n click MassAnalyzerEnum href \"../MassAnalyzerEnum\"\n\n MassSpectrometryConfiguration : mass_spectrometry_acquisition_strategy\n\n MassSpectrometryConfiguration --> \"0..1\" MassSpectrometryAcquisitionStrategyEnum : mass_spectrometry_acquisition_strategy\n click MassSpectrometryAcquisitionStrategyEnum href \"../MassSpectrometryAcquisitionStrategyEnum\"\n\n MassSpectrometryConfiguration : mass_spectrum_collection_modes\n\n MassSpectrometryConfiguration --> \"*\" MassSpectrumCollectionModeEnum : mass_spectrum_collection_modes\n click MassSpectrumCollectionModeEnum href \"../MassSpectrumCollectionModeEnum\"\n\n MassSpectrometryConfiguration : name\n\n MassSpectrometryConfiguration : polarity_mode\n\n MassSpectrometryConfiguration --> \"0..1\" PolarityModeEnum : polarity_mode\n click PolarityModeEnum href \"../PolarityModeEnum\"\n\n MassSpectrometryConfiguration : resolution_categories\n\n MassSpectrometryConfiguration --> \"*\" ResolutionCategoryEnum : resolution_categories\n click ResolutionCategoryEnum href \"../ResolutionCategoryEnum\"\n\n MassSpectrometryConfiguration : type\n\n\n\nname: MassSpectrometryConfiguration\ndescription: A set of parameters that define and control the actions of a mass spectrometry\n process.\nnotes:\n- This class is intended to represent a mass spectrometry method file that controls\n a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslots:\n- mass_spectrometry_acquisition_strategy\n- resolution_categories\n- mass_analyzers\n- ionization_source\n- mass_spectrum_collection_modes\n- polarity_mode\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MassSpectrometryConfiguration\n\nname: MassSpectrometryConfiguration\ndescription: A set of parameters that define and control the actions of a mass spectrometry\n process.\nnotes:\n- This class is intended to represent a mass spectrometry method file that controls\n a mass spectrometry process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Configuration\nslot_usage:\n name:\n name: name\n required: true\n description:\n name: description\n required: true\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n mass_spectrometry_acquisition_strategy:\n name: mass_spectrometry_acquisition_strategy\n description: Mode of running a mass spectrometer method by which m/z ranges are\n selected and ions possibly fragment.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - MS:1003213\n rank: 1000\n alias: mass_spectrometry_acquisition_strategy\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: MassSpectrometryAcquisitionStrategyEnum\n resolution_categories:\n name: resolution_categories\n description: The relative resolution at which spectra were collected.\n examples:\n - value: '[''high'', ''low'']'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: resolution_categories\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: ResolutionCategoryEnum\n multivalued: true\n mass_analyzers:\n name: mass_analyzers\n description: The kind of mass analyzer(s) used during the spectra collection.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - MS:1000443\n rank: 1000\n alias: mass_analyzers\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: MassAnalyzerEnum\n multivalued: true\n ionization_source:\n name: ionization_source\n description: The ionization source used to introduce processed samples into a\n mass spectrometer\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - MS:1000008\n rank: 1000\n alias: ionization_source\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: IonizationSourceEnum\n mass_spectrum_collection_modes:\n name: mass_spectrum_collection_modes\n description: Indicates whether mass spectra were collected in full profile, reduced\n profile, or centroid mode during acquisition.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mass_spectrum_collection_modes\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: MassSpectrumCollectionModeEnum\n multivalued: true\n polarity_mode:\n name: polarity_mode\n description: the polarity of which ions are generated and detected\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: polarity_mode\n owner: MassSpectrometryConfiguration\n domain_of:\n - MassSpectrometryConfiguration\n range: PolarityModeEnum\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MassSpectrometryConfiguration\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MassSpectrometryConfiguration\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n required: true\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MassSpectrometryConfiguration\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n required: true\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MassSpectrometryConfiguration\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MassSpectrometryConfiguration\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MassSpectrometryConfiguration\n\nURI: MassSpectrometryEnum
"},{"location":"MassSpectrometryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metaproteome None metabolome None lipidome None nom None"},{"location":"MassSpectrometryEnum/#slots","title":"Slots","text":"Name Description analyte_category"},{"location":"MassSpectrometryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrometryEnum/#schema-source","title":"Schema Source","text":"name: MassSpectrometryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metaproteome:\n text: metaproteome\n title: Metaproteome\n aliases:\n - metaP\n metabolome:\n text: metabolome\n title: Metabolome\n aliases:\n - metaB\n lipidome:\n text: lipidome\n title: Lipidome\n nom:\n text: nom\n title: Natural Organic Matter\n aliases:\n - natural organic matter\n\nURI: MassSpectrumCollectionModeEnum
"},{"location":"MassSpectrumCollectionModeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description full_profile None reduced_profile None centroid None"},{"location":"MassSpectrumCollectionModeEnum/#slots","title":"Slots","text":"Name Description mass_spectrum_collection_modes Indicates whether mass spectra were collected in full profile, reduced profil..."},{"location":"MassSpectrumCollectionModeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MassSpectrumCollectionModeEnum/#schema-source","title":"Schema Source","text":"name: MassSpectrumCollectionModeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n full_profile:\n text: full_profile\n reduced_profile:\n text: reduced_profile\n centroid:\n text: centroid\n\nNote
This is an abstract class and should not be instantiated directly.
URI: nmdc:MaterialEntity
classDiagram\n class MaterialEntity\n click MaterialEntity href \"../MaterialEntity\"\n NamedThing <|-- MaterialEntity\n click NamedThing href \"../NamedThing\"\n\n\n MaterialEntity <|-- Sample\n click Sample href \"../Sample\"\n MaterialEntity <|-- Site\n click Site href \"../Site\"\n MaterialEntity <|-- Instrument\n click Instrument href \"../Instrument\"\n\n\n\n MaterialEntity : alternative_identifiers\n\n MaterialEntity : description\n\n MaterialEntity : id\n\n MaterialEntity : name\n\n MaterialEntity : type\n\n\n\nname: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nclass_uri: nmdc:MaterialEntity\n\nname: MaterialEntity\ntitle: Material Entity\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Material\n- Physical entity\nis_a: NamedThing\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MaterialEntity\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MaterialEntity\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MaterialEntity\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MaterialEntity\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MaterialEntity\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MaterialEntity\n\nA process that takes one or more samples as inputs and generates one or more samples as outputs.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:MaterialProcessing
classDiagram\n class MaterialProcessing\n click MaterialProcessing href \"../MaterialProcessing\"\n PlannedProcess <|-- MaterialProcessing\n click PlannedProcess href \"../PlannedProcess\"\n\n\n MaterialProcessing <|-- Pooling\n click Pooling href \"../Pooling\"\n MaterialProcessing <|-- Extraction\n click Extraction href \"../Extraction\"\n MaterialProcessing <|-- LibraryPreparation\n click LibraryPreparation href \"../LibraryPreparation\"\n MaterialProcessing <|-- SubSamplingProcess\n click SubSamplingProcess href \"../SubSamplingProcess\"\n MaterialProcessing <|-- MixingProcess\n click MixingProcess href \"../MixingProcess\"\n MaterialProcessing <|-- FiltrationProcess\n click FiltrationProcess href \"../FiltrationProcess\"\n MaterialProcessing <|-- ChromatographicSeparationProcess\n click ChromatographicSeparationProcess href \"../ChromatographicSeparationProcess\"\n MaterialProcessing <|-- DissolvingProcess\n click DissolvingProcess href \"../DissolvingProcess\"\n MaterialProcessing <|-- ChemicalConversionProcess\n click ChemicalConversionProcess href \"../ChemicalConversionProcess\"\n\n\n\n MaterialProcessing : alternative_identifiers\n\n MaterialProcessing : description\n\n MaterialProcessing : end_date\n\n MaterialProcessing : has_failure_categorization\n\n MaterialProcessing --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MaterialProcessing : has_input\n\n MaterialProcessing --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n MaterialProcessing : has_output\n\n MaterialProcessing --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n MaterialProcessing : id\n\n MaterialProcessing : instrument_used\n\n MaterialProcessing --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n MaterialProcessing : name\n\n MaterialProcessing : processing_institution\n\n MaterialProcessing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MaterialProcessing : protocol_link\n\n MaterialProcessing --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MaterialProcessing : qc_comment\n\n MaterialProcessing : qc_status\n\n MaterialProcessing --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MaterialProcessing : start_date\n\n MaterialProcessing : type\n\n\n\nname: MaterialProcessing\ndescription: A process that takes one or more samples as inputs and generates one\n or more samples as outputs.\nnotes:\n- This class is a replacement for BiosampleProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nabstract: true\nslots:\n- instrument_used\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MaterialProcessing\n\nname: MaterialProcessing\ndescription: A process that takes one or more samples as inputs and generates one\n or more samples as outputs.\nnotes:\n- This class is a replacement for BiosampleProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OBI:0000094\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: MaterialProcessing\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MaterialProcessing\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MaterialProcessing\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MaterialProcessing\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MaterialProcessing\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MaterialProcessing\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MaterialProcessing\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MaterialProcessing\n\nURI: MechStrucEnum
"},{"location":"MechStrucEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description subway None coach None carriage None elevator None escalator None boat None train None car None bus None"},{"location":"MechStrucEnum/#slots","title":"Slots","text":"Name Description mech_struc mechanical structure: a moving structure"},{"location":"MechStrucEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MechStrucEnum/#schema-source","title":"Schema Source","text":"name: mech_struc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n subway:\n text: subway\n coach:\n text: coach\n carriage:\n text: carriage\n elevator:\n text: elevator\n escalator:\n text: escalator\n boat:\n text: boat\n train:\n text: train\n car:\n text: car\n bus:\n text: bus\n\nThis is used to link a metabolomics analysis workflow to a specific metabolite
URI: nmdc:MetaboliteIdentification
classDiagram\n class MetaboliteIdentification\n click MetaboliteIdentification href \"../MetaboliteIdentification\"\n\n MetaboliteIdentification : alternative_identifiers\n\n MetaboliteIdentification : highest_similarity_score\n\n MetaboliteIdentification : metabolite_identified\n\n MetaboliteIdentification : type\n\n\n\nname: MetaboliteIdentification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- alternative_identifiers\n- highest_similarity_score\n- metabolite_identified\n- type\nclass_uri: nmdc:MetaboliteIdentification\n\nname: MetaboliteIdentification\ndescription: This is used to link a metabolomics analysis workflow to a specific metabolite\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetaboliteIdentification\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n highest_similarity_score:\n name: highest_similarity_score\n todos:\n - Yuri to fill in description\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: highest_similarity_score\n owner: MetaboliteIdentification\n domain_of:\n - MetaboliteIdentification\n range: float\n metabolite_identified:\n name: metabolite_identified\n description: the specific metabolite identifier\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: metabolite_identified\n owner: MetaboliteIdentification\n domain_of:\n - MetaboliteIdentification\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetaboliteIdentification\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetaboliteIdentification\n\nURI: nmdc:MetabolomicsAnalysis
classDiagram\n class MetabolomicsAnalysis\n click MetabolomicsAnalysis href \"../MetabolomicsAnalysis\"\n WorkflowExecution <|-- MetabolomicsAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetabolomicsAnalysis : alternative_identifiers\n\n MetabolomicsAnalysis : description\n\n MetabolomicsAnalysis : end_date\n\n MetabolomicsAnalysis : ended_at_time\n\n MetabolomicsAnalysis : execution_resource\n\n MetabolomicsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetabolomicsAnalysis : git_url\n\n MetabolomicsAnalysis : has_failure_categorization\n\n MetabolomicsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetabolomicsAnalysis : has_input\n\n MetabolomicsAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetabolomicsAnalysis : has_metabolite_identifications\n\n MetabolomicsAnalysis --> \"*\" MetaboliteIdentification : has_metabolite_identifications\n click MetaboliteIdentification href \"../MetaboliteIdentification\"\n\n MetabolomicsAnalysis : has_output\n\n MetabolomicsAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetabolomicsAnalysis : id\n\n MetabolomicsAnalysis : name\n\n MetabolomicsAnalysis : processing_institution\n\n MetabolomicsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetabolomicsAnalysis : protocol_link\n\n MetabolomicsAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetabolomicsAnalysis : qc_comment\n\n MetabolomicsAnalysis : qc_status\n\n MetabolomicsAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetabolomicsAnalysis : start_date\n\n MetabolomicsAnalysis : started_at_time\n\n MetabolomicsAnalysis : type\n\n MetabolomicsAnalysis : uses_calibration\n\n MetabolomicsAnalysis --> \"0..1\" CalibrationInformation : uses_calibration\n click CalibrationInformation href \"../CalibrationInformation\"\n\n MetabolomicsAnalysis : version\n\n MetabolomicsAnalysis : was_informed_by\n\n MetabolomicsAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetabolomicsAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- has_metabolite_identifications\n- uses_calibration\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetabolomicsAnalysis\n\nname: MetabolomicsAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n has_metabolite_identifications:\n name: has_metabolite_identifications\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_metabolite_identifications\n owner: MetabolomicsAnalysis\n domain_of:\n - MetabolomicsAnalysis\n range: MetaboliteIdentification\n multivalued: true\n inlined: true\n inlined_as_list: true\n uses_calibration:\n name: uses_calibration\n description: calibration information is used by a process\n comments:\n - Retenion index calibration data generated by a gas chromatography mass spectromery\n run is used when analyzing metabolomics data\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: uses_calibration\n owner: MetabolomicsAnalysis\n domain_of:\n - MetabolomicsAnalysis\n - NomAnalysis\n range: CalibrationInformation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetabolomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetabolomicsAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetabolomicsAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmb-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetabolomicsAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetabolomicsAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetabolomicsAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetabolomicsAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetabolomicsAnalysis\n\nThis documentation provides details on the National Microbiome Data Collaborative\u2019s (NMDC) approach to sample and data processing metadata. These are key features that drive the data search and discovery aspect of the NMDC data portal (https://microbiomedata.org/data/). If you are unfamiliar with these types of metadata (Figure 1), we recommend you begin with an Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask) (https://doi.org/10.25979/1607365).
Figure 1: Microbiome metadata types: Information that contextualizes sample including its geographic location and collection date, sample preparation, data processing methods, and data products produced from a biological sample (Luke et al., 2020. Introduction to Metadata and Ontologies: Everything You Always Wanted to Know About Metadata and Ontologies (But Were Afraid to Ask). DOI: 10.25979/1607365).
All data integrated into the NMDC data portal must adhere to existing metadata standards for proper indexing and display, and to ensure accurate search results are returned. This documentation outlines the standards and ontologies that were included in the NMDC data schema, a framework that defines how data were defined and linked. For the 2019-2022 pilot initiative, the NMDC Metadata Standards Team (see the NMDC Team page) leveraged existing community-driven standards developed by the Genomics Standards Consortium (GSC), the Joint Genome Institute (JGI) Genomes Online Database (GOLD), and OBO Foundry\u2019s Environmental Ontology (EnvO). In collaboration with these organizations, the NMDC has created a framework for mapping these standards into an interoperable framework that can be expanded to include additional standards and ontologies in the future.
Additional information on the activities by the NMDC Metadata Standards team can be found on the NMDC website at: https://microbiomedata.org/metadata/
"},{"location":"Metadata_Documentation_Overview/#standards-and-ontologies-used-by-the-nmdc","title":"Standards and Ontologies used by the NMDC","text":""},{"location":"Metadata_Documentation_Overview/#sample-metadata","title":"Sample Metadata","text":""},{"location":"Metadata_Documentation_Overview/#gsc-minimum-information-about-any-x-sequence-mixs","title":"GSC Minimum Information about any (x) Sequence (MIxS)","text":"The GSC has developed standards for describing genomic and metagenomic sequences, including the \u201cminimum information about a genome sequence\u201d (MIGS), the \u201cminimum information about a metagenome sequence\u201d (MIMS), and the \u201cminimum information about a marker gene sequence\u201d (MIMARKS). To complement this community-driven standard effort, the GSC has also developed a system for describing the environment from which a biological sample originates, as \u201cenvironmental packages\u201d and established a unified standard set of checklists through the minimum information about any (x) sequence (MIxS). MIxS provides a standardized data dictionary of sample descriptors (e.g., location, environment, elevation, altitude, depth, etc.) organized into different packages for 17 different sample environments.
To standardize how physical samples are described (i.e., sample metadata, Figure 1), the NMDC Schema includes environmental descriptors from the GSC MIxS standards.
Explore how to create a MIxS-compliant sample metadata spreadsheet
Review our example spreadsheet with sample metadata that has been converted to be compliant with the MIxS Soil environment package. Note that not all non-mandatory terms from the MIxs Soil package were relevant for these example samples, and hence were omitted for clarity.
Basic sample spreadsheet (Tab 1 - before conversion to MIxS)
MIxS-compliant soil spreadsheet (Tab 2 - converted to MIxS Soil)
Explore the mandatory, unique, and shared descriptors from the MIxS Soil package
Searchable descriptors from all MIxS environmental packages - coming soon!
Learn more about all of the 17 MIxS environmental packages
The JGI Genomes OnLine Database (GOLD, Mukherjee 2021) is an open-access repository of genome, metagenome, and metatranscriptome sequencing projects with their associated metadata. GOLD data are organized based on Study, Biosample/Organism, Sequencing Project and Analysis Project (Mukherjee 2017). Biosamples (defined as the physical material collected from an environment) are described using a five-level ecosystem classification path (Figure 2); the NMDC schema also uses this ecosystem classification to describe sample environments.
Figure 2. The GOLD five-level ecosystem classification paths (Mukherjee 2019).
Overview of the GOLD ecosystem paths
Ecosystem describes biosamples using three different broadest contexts, namely environmental, engineered, and host-associated.
Ecosystem category subdivides the ecosystem into categories, such as aquatic or terrestrial.
Ecosystem type classifies those categories into types, such as freshwater or marine, cave, desert, soil, etc.
Ecosystem subtype allows for additional environmental context or boundaries.
Specific ecosystem that describes the environment that directly influences the sample or the environmental material itself.
Explore how to map sample environments using the GOLD ecosystem classification
Learn more about the GOLD ecosystem paths using an interactive visualization tool.
Review a step-by-step example of how to assign the GOLD ecosystem classification to a lake sediment sample.
The Environment Ontology (EnvO, Buttigieg 2016) is a community-led ontology that represents environmental entities such as biomes, environmental features, and environmental materials. Each EnvO term is identified using a unique resource identifier (e.g., CURIE or IRI) that resolves in a web browser. This ensures that EnvO\u2019s terms (and their definitions) are easy to find, reference, and share amongst collaborators. It also ensures that datasets described using EnvO terms can be more easily integrated and analyzed in a reproducible manner. And since the meanings of the terms are precisely defined and accessible, humans and computers can easily connect EnvO terms across datasets.
EnvO terms are the recommended values for several of the mandatory terms in the MIxS packages, often referred to as the \"MIxS triad\u201d.
MIxS: env_broad_scale (a.k.a. Biome): The major environmental system that the sample or specimen came from. Often, the value for this term comes from EnvO\u2019s biome hierarchy, and is similar to GOLD\u2019s Ecosystem category.
MIxS: env_local_scale (a.k.a. Feature): A more direct expression of the sample or specimen\u2019s local vicinity, which likely has a significant influence on the sample or specimen. Possible values are listed in EnvO\u2019s astronomical body part hierarchy, which is similar to GOLD\u2019s Ecosystem type/subtype.
MIxS: env_medium (a.k.a. material): The environmental material(s) immediately surrounding your sample or specimen prior to sampling. Examples of this are found in EnvO\u2019s environmental material hierarchy, and is similar to GOLD\u2019s Specific ecosystem.
Explore how to map sample environments using the EnvO ecosystem classification
Review a step-by-step example of how to assign EnvO terms to an oligotrophic lake sediment sample below.
env_broad_scale (Biome)
Using EnvO biome categories, aquatic is appropriate. However, since the EnvO is a hierarchical system, the aquatic biome has two sub-categories: freshwater and marine biomes. The freshwater biome is further divided into freshwater lake biome and freshwater river biome. Therefore, for a lake sediment sample, freshwater lake biome is the appropriate EnvO biome category.
env_local_scale (Feature)
Next, we describe the local environmental feature in the vicinity of and likely having a strong causal influence on the sample. Using the EnvO astronomical body part categories, we step through the relevant categories (see figure on the right) until we reach the EnvO term oligotrophic lake.
env_medium (Material)
Finally, since the sample is oligotrophic lake sediment, the EnvO environmental material could be assigned sediment. But because the EnvO hierarchy provides sub-categories within sediment, the environmenta material will be assigned lake sediment.
Therefore, the EnvO triad for oligotrophic lake sediment is:
Env_broad_scale: freshwater lake biome [ENVO_01000252]
Env_local_scale: oligotrophic lake [ENVO_01000774]
Env_medium: lake sediment [ENVO_00000546]
"},{"location":"Metadata_Documentation_Overview/#classifying-samples-with-gold-and-mixsenvo","title":"Classifying samples with GOLD and MIxS/EnvO","text":"The five-level GOLD ecosystem classification path and EnvO triad each have unique advantages in describing the environmental context of a biosample. The NMDC leverages the strengths of both the GOLD ecosystem classification path and MIxS/EnvO triad. The assignment of MIxS/EnvO triad for the biosamples currently in the NMDC data portal was achieved through a manual curation process using various metadata fields of GOLD biosamples fields, such as name, description, habitat, sample collection site, identifier, ecosystem classification path, and study description. The NMDC team is currently working on exploring solutions for automated mapping between GOLD and MIxS/EnvO.
Figure 3: Mapping between the MIxS/EnvO triad and the GOLD ecosystem classification enables integration of sample environments defined with GOLD and MIxS/EnvO.
"},{"location":"Metadata_Documentation_Overview/#data-processing-metadata","title":"Data Processing Metadata","text":"In addition, the NMDC is adopting the MIxS standards for sequence data types (e.g., sequencing method, pcr primers and conditions, etc.), and are building on previous efforts by the Proteomics Standards Initiative and Metabolomics Standards Initiative to develop standards and controlled vocabularies for mass spectrometry data types (e.g., ionization mode, mass resolution, scan rate, etc.). Additional details on the processing metadata are coming soon.
"},{"location":"Metadata_Documentation_Overview/#overview-of-the-nmdc-data-schema","title":"Overview of the NMDC Data Schema","text":"The NMDC has developed a normalized metadata schema (available in the NMDC GitHub) for representing studies, samples, relationships between samples, and associated data objects. The schema is organized into object classes, which act as nodes. Each class has associated slots, which are fields that contain metadata that describe the object. For more in-depth information, full documentation of the NMDC Schema can be found here.
For the NMDC pilot, a python toolkit for generating NMDC-compliant JavaScript Object Notation (JSON) objects was developed to create ETL (Extract-Transform-Load) software to ingest metadata from the DOE User Facilities. Read more about the data in the NMDC pilot here.
"},{"location":"MetagenomeAnnotation/","title":"Class: MetagenomeAnnotation","text":"A workflow execution activity that provides functional and structural annotation of assembled metagenome contigs
URI: nmdc:MetagenomeAnnotation
classDiagram\n class MetagenomeAnnotation\n click MetagenomeAnnotation href \"../MetagenomeAnnotation\"\n WorkflowExecution <|-- MetagenomeAnnotation\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetagenomeAnnotation : alternative_identifiers\n\n MetagenomeAnnotation : description\n\n MetagenomeAnnotation : end_date\n\n MetagenomeAnnotation : ended_at_time\n\n MetagenomeAnnotation : execution_resource\n\n MetagenomeAnnotation --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetagenomeAnnotation : git_url\n\n MetagenomeAnnotation : gold_analysis_project_identifiers\n\n MetagenomeAnnotation : has_failure_categorization\n\n MetagenomeAnnotation --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetagenomeAnnotation : has_input\n\n MetagenomeAnnotation --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetagenomeAnnotation : has_output\n\n MetagenomeAnnotation --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetagenomeAnnotation : id\n\n MetagenomeAnnotation : img_identifiers\n\n MetagenomeAnnotation : name\n\n MetagenomeAnnotation : processing_institution\n\n MetagenomeAnnotation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetagenomeAnnotation : protocol_link\n\n MetagenomeAnnotation --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetagenomeAnnotation : qc_comment\n\n MetagenomeAnnotation : qc_status\n\n MetagenomeAnnotation --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetagenomeAnnotation : start_date\n\n MetagenomeAnnotation : started_at_time\n\n MetagenomeAnnotation : type\n\n MetagenomeAnnotation : version\n\n MetagenomeAnnotation : was_informed_by\n\n MetagenomeAnnotation --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetagenomeAnnotation\ndescription: A workflow execution activity that provides functional and structural\n annotation of assembled metagenome contigs\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\n- gold_analysis_project_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\nclass_uri: nmdc:MetagenomeAnnotation\n\nname: MetagenomeAnnotation\ndescription: A workflow execution activity that provides functional and structural\n annotation of assembled metagenome contigs\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\nattributes:\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: MetagenomeAnnotation\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n maximum_cardinality: 1\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n description: identifiers for corresponding analysis projects in GOLD\n examples:\n - value: https://bioregistry.io/gold:Ga0526289\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: analysis_identifiers\n mixins:\n - gold_identifiers\n alias: gold_analysis_project_identifiers\n owner: MetagenomeAnnotation\n domain_of:\n - MetagenomeAnnotation\n - MetatranscriptomeAnnotation\n range: external_identifier\n multivalued: true\n pattern: ^gold:Ga[0-9]+$\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeAnnotation\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetagenomeAnnotation\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeAnnotation\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeAnnotation\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetagenomeAnnotation\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetagenomeAnnotation\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetagenomeAnnotation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetagenomeAnnotation\n\nA workflow execution activity that converts sequencing reads into an assembled metagenome.
URI: nmdc:MetagenomeAssembly
classDiagram\n class MetagenomeAssembly\n click MetagenomeAssembly href \"../MetagenomeAssembly\"\n WorkflowExecution <|-- MetagenomeAssembly\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetagenomeAssembly : alternative_identifiers\n\n MetagenomeAssembly : asm_score\n\n MetagenomeAssembly : contig_bp\n\n MetagenomeAssembly : contigs\n\n MetagenomeAssembly : ctg_l50\n\n MetagenomeAssembly : ctg_l90\n\n MetagenomeAssembly : ctg_logsum\n\n MetagenomeAssembly : ctg_max\n\n MetagenomeAssembly : ctg_n50\n\n MetagenomeAssembly : ctg_n90\n\n MetagenomeAssembly : ctg_powsum\n\n MetagenomeAssembly : description\n\n MetagenomeAssembly : end_date\n\n MetagenomeAssembly : ended_at_time\n\n MetagenomeAssembly : execution_resource\n\n MetagenomeAssembly --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetagenomeAssembly : gap_pct\n\n MetagenomeAssembly : gc_avg\n\n MetagenomeAssembly : gc_std\n\n MetagenomeAssembly : git_url\n\n MetagenomeAssembly : has_failure_categorization\n\n MetagenomeAssembly --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetagenomeAssembly : has_input\n\n MetagenomeAssembly --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetagenomeAssembly : has_output\n\n MetagenomeAssembly --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetagenomeAssembly : id\n\n MetagenomeAssembly : insdc_assembly_identifiers\n\n MetagenomeAssembly : name\n\n MetagenomeAssembly : num_aligned_reads\n\n MetagenomeAssembly : num_input_reads\n\n MetagenomeAssembly : processing_institution\n\n MetagenomeAssembly --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetagenomeAssembly : protocol_link\n\n MetagenomeAssembly --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetagenomeAssembly : qc_comment\n\n MetagenomeAssembly : qc_status\n\n MetagenomeAssembly --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetagenomeAssembly : scaf_bp\n\n MetagenomeAssembly : scaf_l50\n\n MetagenomeAssembly : scaf_l90\n\n MetagenomeAssembly : scaf_l_gt50k\n\n MetagenomeAssembly : scaf_logsum\n\n MetagenomeAssembly : scaf_max\n\n MetagenomeAssembly : scaf_n50\n\n MetagenomeAssembly : scaf_n90\n\n MetagenomeAssembly : scaf_n_gt50k\n\n MetagenomeAssembly : scaf_pct_gt50k\n\n MetagenomeAssembly : scaf_powsum\n\n MetagenomeAssembly : scaffolds\n\n MetagenomeAssembly : start_date\n\n MetagenomeAssembly : started_at_time\n\n MetagenomeAssembly : type\n\n MetagenomeAssembly : version\n\n MetagenomeAssembly : was_informed_by\n\n MetagenomeAssembly --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n relevant to NMDC\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetagenomeAssembly\n\nname: MetagenomeAssembly\ndescription: A workflow execution activity that converts sequencing reads into an\n assembled metagenome.\ncomments:\n- instances of this class may use a de novo assembly strategy in most or all cases\n relevant to NMDC\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n asm_score:\n name: asm_score\n description: A score for comparing metagenomic assembly quality from same sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: asm_score\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaffolds:\n name: scaffolds\n description: Total sequence count of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaffolds\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_logsum:\n name: scaf_logsum\n description: The sum of the (length*log(length)) of all scaffolds, times some\n constant. Increase the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_logsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_powsum:\n name: scaf_powsum\n description: Powersum of all scaffolds is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_powsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_max:\n name: scaf_max\n description: Maximum scaffold length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_max\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_bp:\n name: scaf_bp\n description: Total size in bp of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_bp\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n50:\n name: scaf_n50\n description: Given a set of scaffolds, each with its own length, the N50 count\n is defined as the smallest number of scaffolds whose length sum makes up half\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n90:\n name: scaf_n90\n description: Given a set of scaffolds, each with its own length, the N90 count\n is defined as the smallest number of scaffolds whose length sum makes up 90%\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l50:\n name: scaf_l50\n description: Given a set of scaffolds, the L50 is defined as the sequence length\n of the shortest scaffold at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l90:\n name: scaf_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all scaffolds of that length or longer\n contains at least 90% of the sum of the lengths of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n_gt50k:\n name: scaf_n_gt50k\n description: Total sequence count of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l_gt50k:\n name: scaf_l_gt50k\n description: Total size in bp of all scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_pct_gt50k:\n name: scaf_pct_gt50k\n description: Total sequence size percentage of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_pct_gt50k\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contigs:\n name: contigs\n description: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contigs\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contig_bp:\n name: contig_bp\n description: Total size in bp of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contig_bp\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n50:\n name: ctg_n50\n description: Given a set of contigs, each with its own length, the N50 count is\n defined as the smallest number_of_contigs whose length sum makes up half of\n genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l50:\n name: ctg_l50\n description: Given a set of contigs, the L50 is defined as the sequence length\n of the shortest contig at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l50\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n90:\n name: ctg_n90\n description: Given a set of contigs, each with its own length, the N90 count is\n defined as the smallest number of contigs whose length sum makes up 90% of genome\n size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l90:\n name: ctg_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all contigs of that length or longer\n contains at least 90% of the sum of the lengths of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l90\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_logsum:\n name: ctg_logsum\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_logsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_powsum:\n name: ctg_powsum\n description: Powersum of all contigs is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_powsum\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_max:\n name: ctg_max\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_max\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gap_pct:\n name: gap_pct\n description: The gap size percentage of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gap_pct\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_std:\n name: gc_std\n description: Standard deviation of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_std\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_avg:\n name: gc_avg\n description: Average of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_avg\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_input_reads:\n name: num_input_reads\n description: The sequence count number of input reads for assembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_input_reads\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_aligned_reads:\n name: num_aligned_reads\n description: The sequence count number of input reads aligned to assembled contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_aligned_reads\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n insdc_assembly_identifiers:\n name: insdc_assembly_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: assembly_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_assembly_identifiers\n owner: MetagenomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: string\n pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeAssembly\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetagenomeAssembly\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeAssembly\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmgas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeAssembly\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetagenomeAssembly\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetagenomeAssembly\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetagenomeAssembly\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetagenomeAssembly\n\nInitial sequencing activity that precedes any analysis. This activity has output(s) that are the raw sequencing data.
URI: nmdc:MetagenomeSequencing
classDiagram\n class MetagenomeSequencing\n click MetagenomeSequencing href \"../MetagenomeSequencing\"\n WorkflowExecution <|-- MetagenomeSequencing\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetagenomeSequencing : alternative_identifiers\n\n MetagenomeSequencing : description\n\n MetagenomeSequencing : end_date\n\n MetagenomeSequencing : ended_at_time\n\n MetagenomeSequencing : execution_resource\n\n MetagenomeSequencing --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetagenomeSequencing : git_url\n\n MetagenomeSequencing : has_failure_categorization\n\n MetagenomeSequencing --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetagenomeSequencing : has_input\n\n MetagenomeSequencing --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetagenomeSequencing : has_output\n\n MetagenomeSequencing --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetagenomeSequencing : id\n\n MetagenomeSequencing : name\n\n MetagenomeSequencing : processing_institution\n\n MetagenomeSequencing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetagenomeSequencing : protocol_link\n\n MetagenomeSequencing --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetagenomeSequencing : qc_comment\n\n MetagenomeSequencing : qc_status\n\n MetagenomeSequencing --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetagenomeSequencing : start_date\n\n MetagenomeSequencing : started_at_time\n\n MetagenomeSequencing : type\n\n MetagenomeSequencing : version\n\n MetagenomeSequencing : was_informed_by\n\n MetagenomeSequencing --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetagenomeSequencing\ndescription: Initial sequencing activity that precedes any analysis. This activity\n has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetagenomeSequencing\n\nname: MetagenomeSequencing\ndescription: Initial sequencing activity that precedes any analysis. This activity\n has output(s) that are the raw sequencing data.\ntitle: Metagenome sequencing activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetagenomeSequencing\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetagenomeSequencing\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetagenomeSequencing\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmsa-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetagenomeSequencing\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetagenomeSequencing\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetagenomeSequencing\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetagenomeSequencing\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetagenomeSequencing\n\nURI: nmdc:MetaproteomicsAnalysis
classDiagram\n class MetaproteomicsAnalysis\n click MetaproteomicsAnalysis href \"../MetaproteomicsAnalysis\"\n WorkflowExecution <|-- MetaproteomicsAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetaproteomicsAnalysis : alternative_identifiers\n\n MetaproteomicsAnalysis : description\n\n MetaproteomicsAnalysis : end_date\n\n MetaproteomicsAnalysis : ended_at_time\n\n MetaproteomicsAnalysis : execution_resource\n\n MetaproteomicsAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetaproteomicsAnalysis : git_url\n\n MetaproteomicsAnalysis : has_failure_categorization\n\n MetaproteomicsAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetaproteomicsAnalysis : has_input\n\n MetaproteomicsAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetaproteomicsAnalysis : has_output\n\n MetaproteomicsAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetaproteomicsAnalysis : id\n\n MetaproteomicsAnalysis : metaproteomics_analysis_category\n\n MetaproteomicsAnalysis --> \"1\" MetaproteomicsAnalysisCategoryEnum : metaproteomics_analysis_category\n click MetaproteomicsAnalysisCategoryEnum href \"../MetaproteomicsAnalysisCategoryEnum\"\n\n MetaproteomicsAnalysis : name\n\n MetaproteomicsAnalysis : processing_institution\n\n MetaproteomicsAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetaproteomicsAnalysis : protocol_link\n\n MetaproteomicsAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetaproteomicsAnalysis : qc_comment\n\n MetaproteomicsAnalysis : qc_status\n\n MetaproteomicsAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetaproteomicsAnalysis : start_date\n\n MetaproteomicsAnalysis : started_at_time\n\n MetaproteomicsAnalysis : type\n\n MetaproteomicsAnalysis : version\n\n MetaproteomicsAnalysis : was_informed_by\n\n MetaproteomicsAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetaproteomicsAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- metaproteomics_analysis_category\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetaproteomicsAnalysis\n\nname: MetaproteomicsAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n metaproteomics_analysis_category:\n name: metaproteomics_analysis_category\n description: The category of metaproteomics analysis being performed.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: metaproteomics_analysis_category\n owner: MetaproteomicsAnalysis\n domain_of:\n - MetaproteomicsAnalysis\n range: MetaproteomicsAnalysisCategoryEnum\n required: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetaproteomicsAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetaproteomicsAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetaproteomicsAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmp-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetaproteomicsAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetaproteomicsAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetaproteomicsAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetaproteomicsAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetaproteomicsAnalysis\n\nThe category of metaproteomics analysis being performed.
URI: MetaproteomicsAnalysisCategoryEnum
"},{"location":"MetaproteomicsAnalysisCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description matched_metagenome None A metaproteomics analysis that is matched to a metagenome derived from the sa... in_silico_metagenome None A metaproteomics analysis that is matched to an in silico generated metagenom..."},{"location":"MetaproteomicsAnalysisCategoryEnum/#slots","title":"Slots","text":"Name Description metaproteomics_analysis_category The category of metaproteomics analysis being performed"},{"location":"MetaproteomicsAnalysisCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"MetaproteomicsAnalysisCategoryEnum/#schema-source","title":"Schema Source","text":"name: MetaproteomicsAnalysisCategoryEnum\ndescription: The category of metaproteomics analysis being performed.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n matched_metagenome:\n text: matched_metagenome\n description: A metaproteomics analysis that is matched to a metagenome derived\n from the same biosample.\n in_silico_metagenome:\n text: in_silico_metagenome\n description: A metaproteomics analysis that is matched to an in silico generated\n metagenome.\n\nURI: nmdc:MetatranscriptomeAnnotation
classDiagram\n class MetatranscriptomeAnnotation\n click MetatranscriptomeAnnotation href \"../MetatranscriptomeAnnotation\"\n WorkflowExecution <|-- MetatranscriptomeAnnotation\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetatranscriptomeAnnotation : alternative_identifiers\n\n MetatranscriptomeAnnotation : description\n\n MetatranscriptomeAnnotation : end_date\n\n MetatranscriptomeAnnotation : ended_at_time\n\n MetatranscriptomeAnnotation : execution_resource\n\n MetatranscriptomeAnnotation --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetatranscriptomeAnnotation : git_url\n\n MetatranscriptomeAnnotation : gold_analysis_project_identifiers\n\n MetatranscriptomeAnnotation : has_failure_categorization\n\n MetatranscriptomeAnnotation --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetatranscriptomeAnnotation : has_input\n\n MetatranscriptomeAnnotation --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeAnnotation : has_output\n\n MetatranscriptomeAnnotation --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeAnnotation : id\n\n MetatranscriptomeAnnotation : img_identifiers\n\n MetatranscriptomeAnnotation : name\n\n MetatranscriptomeAnnotation : processing_institution\n\n MetatranscriptomeAnnotation --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetatranscriptomeAnnotation : protocol_link\n\n MetatranscriptomeAnnotation --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetatranscriptomeAnnotation : qc_comment\n\n MetatranscriptomeAnnotation : qc_status\n\n MetatranscriptomeAnnotation --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetatranscriptomeAnnotation : start_date\n\n MetatranscriptomeAnnotation : started_at_time\n\n MetatranscriptomeAnnotation : type\n\n MetatranscriptomeAnnotation : version\n\n MetatranscriptomeAnnotation : was_informed_by\n\n MetatranscriptomeAnnotation --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetatranscriptomeAnnotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\n- gold_analysis_project_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\nclass_uri: nmdc:MetatranscriptomeAnnotation\n\nname: MetatranscriptomeAnnotation\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\nattributes:\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: MetatranscriptomeAnnotation\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n maximum_cardinality: 1\n gold_analysis_project_identifiers:\n name: gold_analysis_project_identifiers\n description: identifiers for corresponding analysis projects in GOLD\n examples:\n - value: https://bioregistry.io/gold:Ga0526289\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: analysis_identifiers\n mixins:\n - gold_identifiers\n alias: gold_analysis_project_identifiers\n owner: MetatranscriptomeAnnotation\n domain_of:\n - MetagenomeAnnotation\n - MetatranscriptomeAnnotation\n range: external_identifier\n multivalued: true\n pattern: ^gold:Ga[0-9]+$\n structured_pattern:\n syntax: ^gold:Ga[0-9]+$\n interpolated: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeAnnotation\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeAnnotation\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtan-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeAnnotation\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetatranscriptomeAnnotation\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetatranscriptomeAnnotation\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetatranscriptomeAnnotation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetatranscriptomeAnnotation\n\nURI: nmdc:MetatranscriptomeAssembly
classDiagram\n class MetatranscriptomeAssembly\n click MetatranscriptomeAssembly href \"../MetatranscriptomeAssembly\"\n WorkflowExecution <|-- MetatranscriptomeAssembly\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetatranscriptomeAssembly : alternative_identifiers\n\n MetatranscriptomeAssembly : asm_score\n\n MetatranscriptomeAssembly : contig_bp\n\n MetatranscriptomeAssembly : contigs\n\n MetatranscriptomeAssembly : ctg_l50\n\n MetatranscriptomeAssembly : ctg_l90\n\n MetatranscriptomeAssembly : ctg_logsum\n\n MetatranscriptomeAssembly : ctg_max\n\n MetatranscriptomeAssembly : ctg_n50\n\n MetatranscriptomeAssembly : ctg_n90\n\n MetatranscriptomeAssembly : ctg_powsum\n\n MetatranscriptomeAssembly : description\n\n MetatranscriptomeAssembly : end_date\n\n MetatranscriptomeAssembly : ended_at_time\n\n MetatranscriptomeAssembly : execution_resource\n\n MetatranscriptomeAssembly --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetatranscriptomeAssembly : gap_pct\n\n MetatranscriptomeAssembly : gc_avg\n\n MetatranscriptomeAssembly : gc_std\n\n MetatranscriptomeAssembly : git_url\n\n MetatranscriptomeAssembly : has_failure_categorization\n\n MetatranscriptomeAssembly --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetatranscriptomeAssembly : has_input\n\n MetatranscriptomeAssembly --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeAssembly : has_output\n\n MetatranscriptomeAssembly --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeAssembly : id\n\n MetatranscriptomeAssembly : insdc_assembly_identifiers\n\n MetatranscriptomeAssembly : name\n\n MetatranscriptomeAssembly : num_aligned_reads\n\n MetatranscriptomeAssembly : num_input_reads\n\n MetatranscriptomeAssembly : processing_institution\n\n MetatranscriptomeAssembly --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetatranscriptomeAssembly : protocol_link\n\n MetatranscriptomeAssembly --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetatranscriptomeAssembly : qc_comment\n\n MetatranscriptomeAssembly : qc_status\n\n MetatranscriptomeAssembly --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetatranscriptomeAssembly : scaf_bp\n\n MetatranscriptomeAssembly : scaf_l50\n\n MetatranscriptomeAssembly : scaf_l90\n\n MetatranscriptomeAssembly : scaf_l_gt50k\n\n MetatranscriptomeAssembly : scaf_logsum\n\n MetatranscriptomeAssembly : scaf_max\n\n MetatranscriptomeAssembly : scaf_n50\n\n MetatranscriptomeAssembly : scaf_n90\n\n MetatranscriptomeAssembly : scaf_n_gt50k\n\n MetatranscriptomeAssembly : scaf_pct_gt50k\n\n MetatranscriptomeAssembly : scaf_powsum\n\n MetatranscriptomeAssembly : scaffolds\n\n MetatranscriptomeAssembly : start_date\n\n MetatranscriptomeAssembly : started_at_time\n\n MetatranscriptomeAssembly : type\n\n MetatranscriptomeAssembly : version\n\n MetatranscriptomeAssembly : was_informed_by\n\n MetatranscriptomeAssembly --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetatranscriptomeAssembly\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- asm_score\n- scaffolds\n- scaf_logsum\n- scaf_powsum\n- scaf_max\n- scaf_bp\n- scaf_n50\n- scaf_n90\n- scaf_l50\n- scaf_l90\n- scaf_n_gt50k\n- scaf_l_gt50k\n- scaf_pct_gt50k\n- contigs\n- contig_bp\n- ctg_n50\n- ctg_l50\n- ctg_n90\n- ctg_l90\n- ctg_logsum\n- ctg_powsum\n- ctg_max\n- gap_pct\n- gc_std\n- gc_avg\n- num_input_reads\n- num_aligned_reads\n- insdc_assembly_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetatranscriptomeAssembly\n\nname: MetatranscriptomeAssembly\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n asm_score:\n name: asm_score\n description: A score for comparing metagenomic assembly quality from same sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: asm_score\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaffolds:\n name: scaffolds\n description: Total sequence count of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaffolds\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_logsum:\n name: scaf_logsum\n description: The sum of the (length*log(length)) of all scaffolds, times some\n constant. Increase the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_logsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_powsum:\n name: scaf_powsum\n description: Powersum of all scaffolds is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_powsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_max:\n name: scaf_max\n description: Maximum scaffold length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_max\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_bp:\n name: scaf_bp\n description: Total size in bp of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_bp\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n50:\n name: scaf_n50\n description: Given a set of scaffolds, each with its own length, the N50 count\n is defined as the smallest number of scaffolds whose length sum makes up half\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n90:\n name: scaf_n90\n description: Given a set of scaffolds, each with its own length, the N90 count\n is defined as the smallest number of scaffolds whose length sum makes up 90%\n of genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l50:\n name: scaf_l50\n description: Given a set of scaffolds, the L50 is defined as the sequence length\n of the shortest scaffold at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l90:\n name: scaf_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all scaffolds of that length or longer\n contains at least 90% of the sum of the lengths of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_n_gt50k:\n name: scaf_n_gt50k\n description: Total sequence count of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_n_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_l_gt50k:\n name: scaf_l_gt50k\n description: Total size in bp of all scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_l_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n scaf_pct_gt50k:\n name: scaf_pct_gt50k\n description: Total sequence size percentage of scaffolds greater than 50 KB.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: scaf_pct_gt50k\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contigs:\n name: contigs\n description: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contigs\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n contig_bp:\n name: contig_bp\n description: Total size in bp of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: contig_bp\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n50:\n name: ctg_n50\n description: Given a set of contigs, each with its own length, the N50 count is\n defined as the smallest number_of_contigs whose length sum makes up half of\n genome size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l50:\n name: ctg_l50\n description: Given a set of contigs, the L50 is defined as the sequence length\n of the shortest contig at 50% of the total genome length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l50\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_n90:\n name: ctg_n90\n description: Given a set of contigs, each with its own length, the N90 count is\n defined as the smallest number of contigs whose length sum makes up 90% of genome\n size.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_n90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_l90:\n name: ctg_l90\n description: The L90 statistic is less than or equal to the L50 statistic; it\n is the length for which the collection of all contigs of that length or longer\n contains at least 90% of the sum of the lengths of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_l90\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_logsum:\n name: ctg_logsum\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_logsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_powsum:\n name: ctg_powsum\n description: Powersum of all contigs is the same as logsum except that it uses\n the sum of (length*(length^P)) for some power P (default P=0.25).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_powsum\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n ctg_max:\n name: ctg_max\n description: Maximum contig length.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: ctg_max\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gap_pct:\n name: gap_pct\n description: The gap size percentage of all scaffolds.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gap_pct\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_std:\n name: gc_std\n description: Standard deviation of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_std\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n gc_avg:\n name: gc_avg\n description: Average of GC content of all contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: gc_avg\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_input_reads:\n name: num_input_reads\n description: The sequence count number of input reads for assembly.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_input_reads\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n num_aligned_reads:\n name: num_aligned_reads\n description: The sequence count number of input reads aligned to assembled contigs.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: metagenome_assembly_parameter\n alias: num_aligned_reads\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: float\n insdc_assembly_identifiers:\n name: insdc_assembly_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: assembly_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_assembly_identifiers\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetagenomeAssembly\n - MetatranscriptomeAssembly\n range: string\n pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeAssembly\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetatranscriptomeAssembly\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeAssembly\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtas-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeAssembly\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetatranscriptomeAssembly\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetatranscriptomeAssembly\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetatranscriptomeAssembly\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetatranscriptomeAssembly\n\nA workflow process that provides expression values and read counts for gene features predicted on the contigs.
URI: nmdc:MetatranscriptomeExpressionAnalysis
classDiagram\n class MetatranscriptomeExpressionAnalysis\n click MetatranscriptomeExpressionAnalysis href \"../MetatranscriptomeExpressionAnalysis\"\n WorkflowExecution <|-- MetatranscriptomeExpressionAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n MetatranscriptomeExpressionAnalysis : alternative_identifiers\n\n MetatranscriptomeExpressionAnalysis : description\n\n MetatranscriptomeExpressionAnalysis : end_date\n\n MetatranscriptomeExpressionAnalysis : ended_at_time\n\n MetatranscriptomeExpressionAnalysis : execution_resource\n\n MetatranscriptomeExpressionAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n MetatranscriptomeExpressionAnalysis : git_url\n\n MetatranscriptomeExpressionAnalysis : has_failure_categorization\n\n MetatranscriptomeExpressionAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MetatranscriptomeExpressionAnalysis : has_input\n\n MetatranscriptomeExpressionAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeExpressionAnalysis : has_output\n\n MetatranscriptomeExpressionAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n MetatranscriptomeExpressionAnalysis : id\n\n MetatranscriptomeExpressionAnalysis : img_identifiers\n\n MetatranscriptomeExpressionAnalysis : name\n\n MetatranscriptomeExpressionAnalysis : processing_institution\n\n MetatranscriptomeExpressionAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MetatranscriptomeExpressionAnalysis : protocol_link\n\n MetatranscriptomeExpressionAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MetatranscriptomeExpressionAnalysis : qc_comment\n\n MetatranscriptomeExpressionAnalysis : qc_status\n\n MetatranscriptomeExpressionAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MetatranscriptomeExpressionAnalysis : start_date\n\n MetatranscriptomeExpressionAnalysis : started_at_time\n\n MetatranscriptomeExpressionAnalysis : type\n\n MetatranscriptomeExpressionAnalysis : version\n\n MetatranscriptomeExpressionAnalysis : was_informed_by\n\n MetatranscriptomeExpressionAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: MetatranscriptomeExpressionAnalysis\ndescription: A workflow process that provides expression values and read counts for\n gene features predicted on the contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- img_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MetatranscriptomeExpressionAnalysis\n\nname: MetatranscriptomeExpressionAnalysis\ndescription: A workflow process that provides expression values and read counts for\n gene features predicted on the contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n img_identifiers:\n name: img_identifiers\n maximum_cardinality: 1\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n img_identifiers:\n name: img_identifiers\n description: A list of identifiers that relate the biosample to records in the\n IMG database.\n title: IMG Identifiers\n todos:\n - add is_a or mixin modeling, like other external_database_identifiers\n - what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n alias: img_identifiers\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - MetagenomeAnnotation\n - Biosample\n - MetatranscriptomeAnnotation\n - MetatranscriptomeExpressionAnalysis\n - MagsAnalysis\n range: external_identifier\n multivalued: true\n pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n maximum_cardinality: 1\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfmtex-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MetatranscriptomeExpressionAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MetatranscriptomeExpressionAnalysis\n\nThe combining of components, particles or layers into a more homogeneous state.
__
URI: nmdc:MixingProcess
classDiagram\n class MixingProcess\n click MixingProcess href \"../MixingProcess\"\n MaterialProcessing <|-- MixingProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n MixingProcess : alternative_identifiers\n\n MixingProcess : description\n\n MixingProcess : duration\n\n MixingProcess --> \"0..1\" QuantityValue : duration\n click QuantityValue href \"../QuantityValue\"\n\n MixingProcess : end_date\n\n MixingProcess : has_failure_categorization\n\n MixingProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n MixingProcess : has_input\n\n MixingProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n MixingProcess : has_output\n\n MixingProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n MixingProcess : id\n\n MixingProcess : instrument_used\n\n MixingProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n MixingProcess : name\n\n MixingProcess : processing_institution\n\n MixingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n MixingProcess : protocol_link\n\n MixingProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n MixingProcess : qc_comment\n\n MixingProcess : qc_status\n\n MixingProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n MixingProcess : start_date\n\n MixingProcess : type\n\n\n\nname: MixingProcess\ndescription: 'The combining of components, particles or layers into a more homogeneous\n state.\n\n '\ncomments:\n- The mixing may be achieved manually or mechanically by shifting the material with\n stirrers or pumps or by revolving or shaking the container.\n- The process must not permit segregation of particles of different size or properties.\n- Homogeneity may be considered to have been achieved in a practical sense when the\n sampling error of the processed portion is negligible compared to the total error\n of the measurement system.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nis_a: MaterialProcessing\nslots:\n- duration\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The mixed sample.\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:MixingProcess\n\nname: MixingProcess\ndescription: 'The combining of components, particles or layers into a more homogeneous\n state.\n\n '\ncomments:\n- The mixing may be achieved manually or mechanically by shifting the material with\n stirrers or pumps or by revolving or shaking the container.\n- The process must not permit segregation of particles of different size or properties.\n- Homogeneity may be considered to have been achieved in a practical sense when the\n sampling error of the processed portion is negligible compared to the total error\n of the measurement system.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The mixed sample.\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n duration:\n name: duration\n description: The elapsed time of an activity.\n examples:\n - value: JsonObj(has_numeric_value=2, has_unit='hours')\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: duration\n owner: MixingProcess\n domain_of:\n - MixingProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: QuantityValue\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: MixingProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The mixed sample.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: MixingProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: MixingProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: MixingProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: MixingProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: MixingProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MixingProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:MixingProcess\n\nA fluid mixture of substances that flow though a chromatographic stationary phase.
URI: nmdc:MobilePhaseSegment
classDiagram\n class MobilePhaseSegment\n click MobilePhaseSegment href \"../MobilePhaseSegment\"\n\n MobilePhaseSegment : duration\n\n MobilePhaseSegment --> \"0..1\" QuantityValue : duration\n click QuantityValue href \"../QuantityValue\"\n\n MobilePhaseSegment : substances_used\n\n MobilePhaseSegment --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n MobilePhaseSegment : type\n\n MobilePhaseSegment : volume\n\n MobilePhaseSegment --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: MobilePhaseSegment\ndescription: A fluid mixture of substances that flow though a chromatographic stationary\n phase.\ncomments:\n- Can be assembled into a list to account for a gradient.\n- Works best for separations that can be accounted for by a series of essentially\n linear changes in the mobile phase composition.\n- For gradients, each segment should declare it's duration.\n- For step-wise separations that might be implemented with a syringe and a cartridge,\n it will probably be more important to assert volumes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- duration\n- substances_used\n- type\n- volume\nclass_uri: nmdc:MobilePhaseSegment\n\nname: MobilePhaseSegment\ndescription: A fluid mixture of substances that flow though a chromatographic stationary\n phase.\ncomments:\n- Can be assembled into a list to account for a gradient.\n- Works best for separations that can be accounted for by a series of essentially\n linear changes in the mobile phase composition.\n- For gradients, each segment should declare it's duration.\n- For step-wise separations that might be implemented with a syringe and a cartridge,\n it will probably be more important to assert volumes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n duration:\n name: duration\n description: The elapsed time of an activity.\n examples:\n - value: JsonObj(has_numeric_value=2, has_unit='hours')\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: duration\n owner: MobilePhaseSegment\n domain_of:\n - MixingProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: QuantityValue\n substances_used:\n name: substances_used\n description: The substances that are combined to enable a ChemicalConversionProcess.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: MobilePhaseSegment\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: MobilePhaseSegment\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n volume:\n name: volume\n description: The volume of a substance.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: MobilePhaseSegment\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\nclass_uri: nmdc:MobilePhaseSegment\n\nThe NMDC Schema is a foundational framework designed to standardize metadata for the National Microbiome Data Collaborative (NMDC) and collaborating data providors. By establishing a structured approach to metadata, the NMDC Schema enables researchers to organize, share, and interpret complex datasets with consistency and clarity. The NMDC Schema is critical substrate used to facilitate interoperability and collaboration, as it provide a common language for data exchange across systems and disciplines. In the context of the NMDC, this schema supports the integration of microbiome data from medicine, agriculture, bioenergy, and environmental science into a cohesive platform.
URI: https://w3id.org/nmdc/nmdc
"},{"location":"NamedThing/","title":"Class: NamedThing","text":"a databased entity or concept/class
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:NamedThing
classDiagram\n class NamedThing\n click NamedThing href \"../NamedThing\"\n NamedThing <|-- GeneProduct\n click GeneProduct href \"../GeneProduct\"\n NamedThing <|-- OntologyClass\n click OntologyClass href \"../OntologyClass\"\n NamedThing <|-- MaterialEntity\n click MaterialEntity href \"../MaterialEntity\"\n NamedThing <|-- PlannedProcess\n click PlannedProcess href \"../PlannedProcess\"\n NamedThing <|-- Study\n click Study href \"../Study\"\n NamedThing <|-- InformationObject\n click InformationObject href \"../InformationObject\"\n\n\n\n NamedThing : alternative_identifiers\n\n NamedThing : description\n\n NamedThing : id\n\n NamedThing : name\n\n NamedThing : type\n\n\n\nname: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nslots:\n- id\n- name\n- description\n- alternative_identifiers\n- type\nclass_uri: nmdc:NamedThing\n\nname: NamedThing\ndescription: a databased entity or concept/class\nfrom_schema: https://w3id.org/nmdc/nmdc\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: NamedThing\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NamedThing\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: NamedThing\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: NamedThing\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: NamedThing\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:NamedThing\n\nPrefix part of CURIE
URI: xsd:string
base: NCName
uri: xsd:string
repr: str
A URI, CURIE or BNODE that represents a node in a model.
URI: shex:nonLiteral
base: NodeIdentifier
uri: shex:nonLiteral
repr: str
URI: nmdc:NomAnalysis
classDiagram\n class NomAnalysis\n click NomAnalysis href \"../NomAnalysis\"\n WorkflowExecution <|-- NomAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n NomAnalysis : alternative_identifiers\n\n NomAnalysis : description\n\n NomAnalysis : end_date\n\n NomAnalysis : ended_at_time\n\n NomAnalysis : execution_resource\n\n NomAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n NomAnalysis : git_url\n\n NomAnalysis : has_failure_categorization\n\n NomAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n NomAnalysis : has_input\n\n NomAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n NomAnalysis : has_output\n\n NomAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n NomAnalysis : id\n\n NomAnalysis : name\n\n NomAnalysis : processing_institution\n\n NomAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n NomAnalysis : protocol_link\n\n NomAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n NomAnalysis : qc_comment\n\n NomAnalysis : qc_status\n\n NomAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n NomAnalysis : start_date\n\n NomAnalysis : started_at_time\n\n NomAnalysis : type\n\n NomAnalysis : uses_calibration\n\n NomAnalysis --> \"0..1\" CalibrationInformation : uses_calibration\n click CalibrationInformation href \"../CalibrationInformation\"\n\n NomAnalysis : version\n\n NomAnalysis : was_informed_by\n\n NomAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: NomAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- uses_calibration\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:NomAnalysis\n\nname: NomAnalysis\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n uses_calibration:\n name: uses_calibration\n description: calibration information is used by a process\n comments:\n - Retenion index calibration data generated by a gas chromatography mass spectromery\n run is used when analyzing metabolomics data\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: uses_calibration\n owner: NomAnalysis\n domain_of:\n - MetabolomicsAnalysis\n - NomAnalysis\n range: CalibrationInformation\n structured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: NomAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgms)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: NomAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: NomAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfnom-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NomAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: NomAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: NomAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: NomAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:NomAnalysis\n\nA DataGeneration in which the sequence of DNA or RNA molecules is generated.
URI: nmdc:NucleotideSequencing
classDiagram\n class NucleotideSequencing\n click NucleotideSequencing href \"../NucleotideSequencing\"\n DataGeneration <|-- NucleotideSequencing\n click DataGeneration href \"../DataGeneration\"\n\n\n\n NucleotideSequencing : add_date\n\n NucleotideSequencing : alternative_identifiers\n\n NucleotideSequencing : analyte_category\n\n NucleotideSequencing --> \"1\" NucleotideSequencingEnum : analyte_category\n click NucleotideSequencingEnum href \"../NucleotideSequencingEnum\"\n\n NucleotideSequencing : associated_studies\n\n NucleotideSequencing --> \"1..*\" Study : associated_studies\n click Study href \"../Study\"\n\n NucleotideSequencing : description\n\n NucleotideSequencing : end_date\n\n NucleotideSequencing : gold_sequencing_project_identifiers\n\n NucleotideSequencing : has_failure_categorization\n\n NucleotideSequencing --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n NucleotideSequencing : has_input\n\n NucleotideSequencing --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n NucleotideSequencing : has_output\n\n NucleotideSequencing --> \"*\" DataObject : has_output\n click DataObject href \"../DataObject\"\n\n NucleotideSequencing : id\n\n NucleotideSequencing : insdc_bioproject_identifiers\n\n NucleotideSequencing : insdc_experiment_identifiers\n\n NucleotideSequencing : instrument_used\n\n NucleotideSequencing --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n NucleotideSequencing : mod_date\n\n NucleotideSequencing : name\n\n NucleotideSequencing : ncbi_project_name\n\n NucleotideSequencing : principal_investigator\n\n NucleotideSequencing --> \"0..1\" PersonValue : principal_investigator\n click PersonValue href \"../PersonValue\"\n\n NucleotideSequencing : processing_institution\n\n NucleotideSequencing --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n NucleotideSequencing : protocol_link\n\n NucleotideSequencing --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n NucleotideSequencing : qc_comment\n\n NucleotideSequencing : qc_status\n\n NucleotideSequencing --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n NucleotideSequencing : start_date\n\n NucleotideSequencing : target_gene\n\n NucleotideSequencing --> \"0..1\" TargetGeneEnum : target_gene\n click TargetGeneEnum href \"../TargetGeneEnum\"\n\n NucleotideSequencing : target_subfragment\n\n NucleotideSequencing --> \"0..1\" TextValue : target_subfragment\n click TextValue href \"../TextValue\"\n\n NucleotideSequencing : type\n\n\n\nname: NucleotideSequencing\ndescription: A DataGeneration in which the sequence of DNA or RNA molecules is generated.\ncomments:\n- For example data generated from an Illumina or Pacific Biosciences instrument.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: DataGeneration\nslots:\n- gold_sequencing_project_identifiers\n- insdc_bioproject_identifiers\n- insdc_experiment_identifiers\n- ncbi_project_name\n- target_gene\n- target_subfragment\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n analyte_category:\n name: analyte_category\n range: NucleotideSequencingEnum\nclass_uri: nmdc:NucleotideSequencing\n\nname: NucleotideSequencing\ndescription: A DataGeneration in which the sequence of DNA or RNA molecules is generated.\ncomments:\n- For example data generated from an Illumina or Pacific Biosciences instrument.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: DataGeneration\nslot_usage:\n id:\n name: id\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n analyte_category:\n name: analyte_category\n range: NucleotideSequencingEnum\nattributes:\n gold_sequencing_project_identifiers:\n name: gold_sequencing_project_identifiers\n description: identifiers for corresponding sequencing project in GOLD\n examples:\n - value: https://bioregistry.io/gold:Gp0108335\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: omics_processing_identifiers\n mixins:\n - gold_identifiers\n alias: gold_sequencing_project_identifiers\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n range: external_identifier\n multivalued: true\n pattern: ^gold:Gp[0-9]+$\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n description: identifiers for corresponding project in INSDC Bioproject\n comments:\n - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n one to one\n examples:\n - value: https://bioregistry.io/bioproject:PRJNA366857\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2\n metatranscriptome\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ncbi.nlm.nih.gov/bioproject/\n - https://www.ddbj.nig.ac.jp/bioproject/index-e.html\n aliases:\n - NCBI bioproject identifiers\n - DDBJ bioproject identifiers\n rank: 1000\n is_a: study_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_bioproject_identifiers\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n insdc_experiment_identifiers:\n name: insdc_experiment_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: external_database_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_experiment_identifiers\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n - DataObject\n range: external_identifier\n multivalued: true\n pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n ncbi_project_name:\n name: ncbi_project_name\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: ncbi_project_name\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n range: string\n target_gene:\n name: target_gene\n annotations:\n expected_value:\n tag: expected_value\n value: gene name\n description: Targeted gene or locus name for marker gene studies\n title: target gene\n examples:\n - value: 16S rRNA, 18S rRNA, nif, amoA, rpo\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target gene\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000044\n alias: target_gene\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n range: TargetGeneEnum\n multivalued: false\n target_subfragment:\n name: target_subfragment\n annotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\n description: Name of subfragment of a gene or locus. Important to e.g. identify\n special regions on marker genes like V6 on 16S rRNA\n title: target subfragment\n examples:\n - value: V6, V9, ITS\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - target subfragment\n rank: 1000\n is_a: sequencing field\n string_serialization: '{text}'\n slot_uri: MIXS:0000045\n alias: target_subfragment\n owner: NucleotideSequencing\n domain_of:\n - NucleotideSequencing\n range: TextValue\n multivalued: false\n add_date:\n name: add_date\n description: The date on which the information was added to the database.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: add_date\n owner: NucleotideSequencing\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n analyte_category:\n name: analyte_category\n description: \"The type of analyte(s) that were measured in the data generation\\\n \\ process and analyzed\\n in the Workflow Chain\\n\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: analyte_category\n owner: NucleotideSequencing\n domain_of:\n - DataGeneration\n range: NucleotideSequencingEnum\n required: true\n associated_studies:\n name: associated_studies\n description: The study associated with a resource.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: associated_studies\n owner: NucleotideSequencing\n domain_of:\n - Biosample\n - DataGeneration\n range: Study\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(sty)-{id_shoulder}-{id_blade}$'\n interpolated: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: NucleotideSequencing\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n mod_date:\n name: mod_date\n description: The last date on which the database information was modified.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: mod_date\n owner: NucleotideSequencing\n domain_of:\n - Biosample\n - DataGeneration\n range: string\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n alias: principal_investigator\n owner: NucleotideSequencing\n domain_of:\n - Study\n - DataGeneration\n range: PersonValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: DataObject\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: NucleotideSequencing\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: NucleotideSequencing\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dgns|omprc)-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: NucleotideSequencing\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: NucleotideSequencing\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: NucleotideSequencing\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: NucleotideSequencing\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:NucleotideSequencing\n\nURI: NucleotideSequencingEnum
"},{"location":"NucleotideSequencingEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description metagenome None metatranscriptome None amplicon_sequencing_assay OBI:0002767"},{"location":"NucleotideSequencingEnum/#slots","title":"Slots","text":"Name Description analyte_category"},{"location":"NucleotideSequencingEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"NucleotideSequencingEnum/#schema-source","title":"Schema Source","text":"name: NucleotideSequencingEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n metagenome:\n text: metagenome\n title: Metagenome\n aliases:\n - metaG\n metatranscriptome:\n text: metatranscriptome\n title: Metatranscriptome\n aliases:\n - metaT\n amplicon_sequencing_assay:\n text: amplicon_sequencing_assay\n meaning: OBI:0002767\n title: Amplicon\n\nA URI or CURIE that represents an object in the model.
URI: shex:iri
base: ElementIdentifier
uri: shex:iri
repr: str
URI: OccupDocumentEnum
"},{"location":"OccupDocumentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description automated count None estimate None manual count None videos None"},{"location":"OccupDocumentEnum/#slots","title":"Slots","text":"Name Description occup_document The type of documentation of occupancy"},{"location":"OccupDocumentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OccupDocumentEnum/#schema-source","title":"Schema Source","text":"name: occup_document_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n automated count:\n text: automated count\n estimate:\n text: estimate\n manual count:\n text: manual count\n videos:\n text: videos\n\nA representation of class defined in an external ontology.
URI: nmdc:OntologyClass
classDiagram\n class OntologyClass\n click OntologyClass href \"../OntologyClass\"\n NamedThing <|-- OntologyClass\n click NamedThing href \"../NamedThing\"\n\n\n OntologyClass <|-- EnvironmentalMaterialTerm\n click EnvironmentalMaterialTerm href \"../EnvironmentalMaterialTerm\"\n OntologyClass <|-- ChemicalEntity\n click ChemicalEntity href \"../ChemicalEntity\"\n OntologyClass <|-- FunctionalAnnotationTerm\n click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n OntologyClass : alternative_identifiers\n\n OntologyClass : alternative_names\n\n OntologyClass : definition\n\n OntologyClass : description\n\n OntologyClass : id\n\n OntologyClass : name\n\n OntologyClass : relations\n\n OntologyClass --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n OntologyClass : type\n\n\n\nname: OntologyClass\ndescription: A representation of class defined in an external ontology.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:OntologyClass\n- owl:Class\n- schema:Class\nis_a: NamedThing\nslots:\n- alternative_names\nslot_usage:\n id:\n name: id\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nattributes:\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\nclass_uri: nmdc:OntologyClass\n\nname: OntologyClass\ndescription: A representation of class defined in an external ontology.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:OntologyClass\n- owl:Class\n- schema:Class\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\nattributes:\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: OntologyClass\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: OntologyClass\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: OntologyClass\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: OntologyClass\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OntologyClass\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OntologyClass\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: OntologyClass\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: OntologyClass\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:OntologyClass\n\nA relationship between two ontology classes as specified either directly in the ontology in the form of axioms (statements or assertions that defines rules or constraints in an ontology) or inferred via reasoning. The association object is defined by two terms (the subject and the object) and the relationship between them (the predicate). Because ontologies often have a plethora of relationships/axiom types and can have additional metadata on the relationship itself, these kinds of relationships are structured as a class instead of a simple set of slots on OntologyClass itself.
URI: nmdc:OntologyRelation
classDiagram\n class OntologyRelation\n click OntologyRelation href \"../OntologyRelation\"\n\n OntologyRelation : object\n\n OntologyRelation --> \"1\" OntologyClass : object\n click OntologyClass href \"../OntologyClass\"\n\n OntologyRelation : predicate\n\n OntologyRelation --> \"1\" OntologyClass : predicate\n click OntologyClass href \"../OntologyClass\"\n\n OntologyRelation : subject\n\n OntologyRelation --> \"1\" OntologyClass : subject\n click OntologyClass href \"../OntologyClass\"\n\n OntologyRelation : type\n\n\n\nOntologyClass as defined below). Not all ontology axioms (associations) between terms need to be ingested into the NMDC data stores. In general, subclass_of and part_of relationships/axioms are often good default relations/associations to support ontology browsing in user interfaces.name: OntologyRelation\ndescription: A relationship between two ontology classes as specified either directly\n in the ontology in the form of axioms (statements or assertions that defines rules\n or constraints in an ontology) or inferred via reasoning. The association object\n is defined by two terms (the subject and the object) and the relationship between\n them (the predicate). Because ontologies often have a plethora of relationships/axiom\n types and can have additional metadata on the relationship itself, these kinds of\n relationships are structured as a class instead of a simple set of slots on OntologyClass\n itself.\ncomments:\n- 'For example, the relationship between ''soil'' and ''enriched soil'' in the Environmental\n Ontology (ENVO) is defined by the following axioms: ''enriched soil'' subclass_of\n ''soil'', and ''enriched soil'' has_increased_levels_of (some) ''material entity.'' Converting\n these stat\u2202ements to OntologyAssociations so they can be used in the NMDC data\n stores, the subject of the first axiom or statement, would be ''soil'', the predicate\n would be ''subclass_of'', and the object would be ''enriched soil''. For the second\n axiom, the subject would be ''enriched soil'', the predicate would be ''has_increased_levels_of'',\n and the object would be ''material entity.'' (Note that text labels are used in\n this example for ease of understanding and the literal values of subject, predicate,\n and object in this class will be the id (curie) of the `OntologyClass` as defined\n below). Not all ontology axioms (associations) between terms need to be ingested\n into the NMDC data stores. In general, subclass_of and part_of relationships/axioms\n are often good default relations/associations to support ontology browsing in user\n interfaces.'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OntologyAssociation\nslots:\n- type\nattributes:\n subject:\n name: subject\n from_schema: https://w3id.org/nmdc/basic_classes\n domain_of:\n - FunctionalAnnotation\n - OntologyRelation\n range: OntologyClass\n required: true\n predicate:\n name: predicate\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n domain_of:\n - OntologyRelation\n range: OntologyClass\n required: true\n object:\n name: object\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n domain_of:\n - OntologyRelation\n range: OntologyClass\n required: true\nclass_uri: nmdc:OntologyRelation\n\nname: OntologyRelation\ndescription: A relationship between two ontology classes as specified either directly\n in the ontology in the form of axioms (statements or assertions that defines rules\n or constraints in an ontology) or inferred via reasoning. The association object\n is defined by two terms (the subject and the object) and the relationship between\n them (the predicate). Because ontologies often have a plethora of relationships/axiom\n types and can have additional metadata on the relationship itself, these kinds of\n relationships are structured as a class instead of a simple set of slots on OntologyClass\n itself.\ncomments:\n- 'For example, the relationship between ''soil'' and ''enriched soil'' in the Environmental\n Ontology (ENVO) is defined by the following axioms: ''enriched soil'' subclass_of\n ''soil'', and ''enriched soil'' has_increased_levels_of (some) ''material entity.'' Converting\n these stat\u2202ements to OntologyAssociations so they can be used in the NMDC data\n stores, the subject of the first axiom or statement, would be ''soil'', the predicate\n would be ''subclass_of'', and the object would be ''enriched soil''. For the second\n axiom, the subject would be ''enriched soil'', the predicate would be ''has_increased_levels_of'',\n and the object would be ''material entity.'' (Note that text labels are used in\n this example for ease of understanding and the literal values of subject, predicate,\n and object in this class will be the id (curie) of the `OntologyClass` as defined\n below). Not all ontology axioms (associations) between terms need to be ingested\n into the NMDC data stores. In general, subclass_of and part_of relationships/axioms\n are often good default relations/associations to support ontology browsing in user\n interfaces.'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- OntologyAssociation\nattributes:\n subject:\n name: subject\n from_schema: https://w3id.org/nmdc/basic_classes\n alias: subject\n owner: OntologyRelation\n domain_of:\n - FunctionalAnnotation\n - OntologyRelation\n range: OntologyClass\n required: true\n predicate:\n name: predicate\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: predicate\n owner: OntologyRelation\n domain_of:\n - OntologyRelation\n range: OntologyClass\n required: true\n object:\n name: object\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: object\n owner: OntologyRelation\n domain_of:\n - OntologyRelation\n range: OntologyClass\n required: true\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: OntologyRelation\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:OntologyRelation\n\nURI: OrganismCountEnum
"},{"location":"OrganismCountEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ATP None MPN None other None"},{"location":"OrganismCountEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OrganismCountEnum/#schema-source","title":"Schema Source","text":"name: organism_count_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n ATP:\n text: ATP\n MPN:\n text: MPN\n other:\n text: other\n\nA set of genes or gene products in which all members are orthologous
URI: nmdc:OrthologyGroup
classDiagram\n class OrthologyGroup\n click OrthologyGroup href \"../OrthologyGroup\"\n FunctionalAnnotationTerm <|-- OrthologyGroup\n click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n OrthologyGroup : alternative_identifiers\n\n OrthologyGroup : alternative_names\n\n OrthologyGroup : definition\n\n OrthologyGroup : description\n\n OrthologyGroup : id\n\n OrthologyGroup : name\n\n OrthologyGroup : relations\n\n OrthologyGroup --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n OrthologyGroup : type\n\n\n\nInstances of this class should have identifiers with one of the following prefixes:
CATH
EGGNOG
KEGG.ORTHOLOGY
PANTHER.FAMILY
PFAM
SUPFAM
TIGRFAM
name: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\ntodos:\n- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable\n in the Data Portal?\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nclass_uri: nmdc:OrthologyGroup\n\nname: OrthologyGroup\nid_prefixes:\n- CATH\n- EGGNOG\n- KEGG.ORTHOLOGY\n- PANTHER.FAMILY\n- PFAM\n- SUPFAM\n- TIGRFAM\ndescription: A set of genes or gene products in which all members are orthologous\ntodos:\n- is OrthologyGroup instantiated in an MongoDB collection? Aren't Pathways searchable\n in the Data Portal?\nnotes:\n- KEGG.ORTHOLOGY prefix is used for KO numbers\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:GeneFamily\nis_a: FunctionalAnnotationTerm\nattributes:\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: OrthologyGroup\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: OrthologyGroup\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: OrthologyGroup\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: OrthologyGroup\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: OrthologyGroup\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: OrthologyGroup\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: OrthologyGroup\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: OrthologyGroup\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:OrthologyGroup\n\nURI: OxyStatSampEnum
"},{"location":"OxyStatSampEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description aerobic None anaerobic None other None"},{"location":"OxyStatSampEnum/#slots","title":"Slots","text":"Name Description oxy_stat_samp Oxygenation status of sample"},{"location":"OxyStatSampEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"OxyStatSampEnum/#schema-source","title":"Schema Source","text":"name: oxy_stat_samp_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n aerobic:\n text: aerobic\n anaerobic:\n text: anaerobic\n other:\n text: other\n\nA pathway is a sequence of steps/reactions carried out by an organism or community of organisms
URI: nmdc:Pathway
classDiagram\n class Pathway\n click Pathway href \"../Pathway\"\n FunctionalAnnotationTerm <|-- Pathway\n click FunctionalAnnotationTerm href \"../FunctionalAnnotationTerm\"\n\n\n\n Pathway : alternative_identifiers\n\n Pathway : alternative_names\n\n Pathway : definition\n\n Pathway : description\n\n Pathway : id\n\n Pathway : name\n\n Pathway : relations\n\n Pathway --> \"*\" OntologyRelation : relations\n click OntologyRelation href \"../OntologyRelation\"\n\n Pathway : type\n\n\n\nInstances of this class should have identifiers with one of the following prefixes:
KEGG_PATHWAY
COG
name: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n or community of organisms\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\ntodos:\n- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable\n part_of a Pathway\n- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in\n the Data Portal?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nclass_uri: nmdc:Pathway\n\nname: Pathway\nid_prefixes:\n- KEGG_PATHWAY\n- COG\ndescription: A pathway is a sequence of steps/reactions carried out by an organism\n or community of organisms\ndeprecated: not used. 2024-07-10 https://github.com/microbiomedata/nmdc-schema/issues/1881\ntodos:\n- If we reverted to including Reaction in the schema, then a Reaction would be a reasonable\n part_of a Pathway\n- is Pathway instantiated in an MongoDB collection? Aren't Pathways searchable in\n the Data Portal?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological process\n- metabolic pathway\n- signaling pathway\nexact_mappings:\n- biolink:Pathway\nis_a: FunctionalAnnotationTerm\nattributes:\n alternative_names:\n name: alternative_names\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: Pathway\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n definition:\n name: definition\n description: The definition of the ontology term as provided by the ontology.\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: definition\n owner: Pathway\n domain_of:\n - OntologyClass\n range: string\n relations:\n name: relations\n from_schema: https://w3id.org/nmdc/basic_classes\n rank: 1000\n alias: relations\n owner: Pathway\n domain_of:\n - OntologyClass\n range: OntologyRelation\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - The identifiers for terms from external ontologies can't have their ids constrained\n to the nmdc namespace\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Pathway\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Pathway\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Pathway\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Pathway\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Pathway\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Pathway\n\nThis is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information
URI: nmdc:PeptideQuantification
classDiagram\n class PeptideQuantification\n click PeptideQuantification href \"../PeptideQuantification\"\n\n PeptideQuantification : all_proteins\n\n PeptideQuantification --> \"*\" GeneProduct : all_proteins\n click GeneProduct href \"../GeneProduct\"\n\n PeptideQuantification : best_protein\n\n PeptideQuantification --> \"0..1\" GeneProduct : best_protein\n click GeneProduct href \"../GeneProduct\"\n\n PeptideQuantification : min_q_value\n\n PeptideQuantification : peptide_sequence\n\n PeptideQuantification : peptide_spectral_count\n\n PeptideQuantification : peptide_sum_masic_abundance\n\n PeptideQuantification : type\n\n\n\nname: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n peptide sequence and related information\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- type\n- all_proteins\n- best_protein\n- min_q_value\n- peptide_sequence\n- peptide_spectral_count\n- peptide_sum_masic_abundance\nclass_uri: nmdc:PeptideQuantification\n\nname: PeptideQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n peptide sequence and related information\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: PeptideQuantification\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n all_proteins:\n name: all_proteins\n description: the list of protein identifiers that are associated with the peptide\n sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: all_proteins\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n multivalued: true\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly associated with the\n peptide sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: best_protein\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n min_q_value:\n name: min_q_value\n description: smallest Q-Value associated with the peptide sequence as provided\n by MSGFPlus tool\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - OBI:0001442\n rank: 1000\n alias: min_q_value\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: float\n peptide_sequence:\n name: peptide_sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sequence\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: string\n peptide_spectral_count:\n name: peptide_spectral_count\n description: sum of filter passing MS2 spectra associated with the peptide sequence\n within a given LC-MS/MS data file\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_spectral_count\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: integer\n peptide_sum_masic_abundance:\n name: peptide_sum_masic_abundance\n description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n associated with the peptide sequence from a given LC-MS/MS data file using the\n MASIC tool\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sum_masic_abundance\n owner: PeptideQuantification\n domain_of:\n - PeptideQuantification\n range: integer\nclass_uri: nmdc:PeptideQuantification\n\nAn attribute value representing a person
URI: nmdc:PersonValue
classDiagram\n class PersonValue\n click PersonValue href \"../PersonValue\"\n AttributeValue <|-- PersonValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n PersonValue : email\n\n PersonValue : has_raw_value\n\n PersonValue : name\n\n PersonValue : orcid\n\n PersonValue : profile_image_url\n\n PersonValue : type\n\n PersonValue : websites\n\n\n\nname: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- email\n- name\n- orcid\n- profile_image_url\n- websites\nslot_usage:\n orcid:\n name: orcid\n annotations:\n tooltip:\n tag: tooltip\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n email:\n name: email\n annotations:\n tooltip:\n tag: tooltip\n value: Email address for this person.\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\nclass_uri: nmdc:PersonValue\n\nname: PersonValue\ndescription: An attribute value representing a person\ntodos:\n- add additional fields e.g for institution\n- deprecate \"has_raw_value\" in favor of \"name\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslot_usage:\n orcid:\n name: orcid\n annotations:\n tooltip:\n tag: tooltip\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n email:\n name: email\n annotations:\n tooltip:\n tag: tooltip\n value: Email address for this person.\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\nattributes:\n email:\n name: email\n annotations:\n tooltip:\n tag: tooltip\n value: Email address for this person.\n description: An email address for an entity such as a person. This should be the\n primary email address used.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: schema:email\n alias: email\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: First name, middle initial, and last name of this person.\n description: The full name of the Investigator. It should follow the format FIRST\n [MIDDLE NAME| MIDDLE INITIAL] LAST, where MIDDLE NAME| MIDDLE INITIAL is optional.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: PersonValue\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n orcid:\n name: orcid\n annotations:\n tooltip:\n tag: tooltip\n value: Open Researcher and Contributor ID for this person. See https://orcid.org\n description: The ORCID of a person.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: orcid\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n profile_image_url:\n name: profile_image_url\n description: A url that points to an image of a person.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: profile_image_url\n owner: PersonValue\n domain_of:\n - PersonValue\n range: string\n websites:\n name: websites\n description: A list of websites that are associated with the entity.\n comments:\n - DOIs should not be included as websites. Instead, use the associated_dois slot.\n - A consortium's homepage website should be included in the homepage_website slot,\n not in websites.\n - consortium is a convenience term for a Study whose study_category value is consortium\n - the website slot and its subproperties are virtually identical to the url slot,\n except that they are multivalued and url is single-valued.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:url\n rank: 1000\n alias: websites\n owner: PersonValue\n domain_of:\n - PersonValue\n - Study\n range: string\n multivalued: true\n pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n has_raw_value:\n name: has_raw_value\n description: The full name of the Investigator in format FIRST LAST.\n notes:\n - May eventually be deprecated in favor of \"name\".\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: PersonValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: PersonValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:PersonValue\n\nNote
This is an abstract class and should not be instantiated directly.
URI: OBI:0000011
classDiagram\n class PlannedProcess\n click PlannedProcess href \"../PlannedProcess\"\n NamedThing <|-- PlannedProcess\n click NamedThing href \"../NamedThing\"\n\n\n PlannedProcess <|-- CollectingBiosamplesFromSite\n click CollectingBiosamplesFromSite href \"../CollectingBiosamplesFromSite\"\n PlannedProcess <|-- ProtocolExecution\n click ProtocolExecution href \"../ProtocolExecution\"\n PlannedProcess <|-- StorageProcess\n click StorageProcess href \"../StorageProcess\"\n PlannedProcess <|-- MaterialProcessing\n click MaterialProcessing href \"../MaterialProcessing\"\n PlannedProcess <|-- DataGeneration\n click DataGeneration href \"../DataGeneration\"\n PlannedProcess <|-- WorkflowExecution\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n PlannedProcess : alternative_identifiers\n\n PlannedProcess : description\n\n PlannedProcess : end_date\n\n PlannedProcess : has_failure_categorization\n\n PlannedProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n PlannedProcess : has_input\n\n PlannedProcess --> \"*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n PlannedProcess : has_output\n\n PlannedProcess --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n PlannedProcess : id\n\n PlannedProcess : name\n\n PlannedProcess : processing_institution\n\n PlannedProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n PlannedProcess : protocol_link\n\n PlannedProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n PlannedProcess : qc_comment\n\n PlannedProcess : qc_status\n\n PlannedProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n PlannedProcess : start_date\n\n PlannedProcess : type\n\n\n\nname: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nslots:\n- has_input\n- has_output\n- processing_institution\n- protocol_link\n- start_date\n- end_date\n- qc_status\n- qc_comment\n- has_failure_categorization\nclass_uri: OBI:0000011\n\nname: PlannedProcess\ntitle: Planned Process\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: NamedThing\nabstract: true\nattributes:\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: PlannedProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: PlannedProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: PlannedProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: PlannedProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: PlannedProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: PlannedProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: OBI:0000011\n\nURI: PlantGrowthMedEnum
"},{"location":"PlantGrowthMedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description other artificial liquid medium None other artificial solid medium None peat moss None perlite None pumice None sand None soil None vermiculite None water None"},{"location":"PlantGrowthMedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantGrowthMedEnum/#schema-source","title":"Schema Source","text":"name: plant_growth_med_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n other artificial liquid medium:\n text: other artificial liquid medium\n other artificial solid medium:\n text: other artificial solid medium\n peat moss:\n text: peat moss\n perlite:\n text: perlite\n pumice:\n text: pumice\n sand:\n text: sand\n soil:\n text: soil\n vermiculite:\n text: vermiculite\n water:\n text: water\n\nURI: PlantSexEnum
"},{"location":"PlantSexEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Androdioecious None Androecious None Androgynous None Androgynomonoecious None Andromonoecious None Bisexual None Dichogamous None Diclinous None Dioecious None Gynodioecious None Gynoecious None Gynomonoecious None Hermaphroditic None Imperfect None Monoclinous None Monoecious None Perfect None Polygamodioecious None Polygamomonoecious None Polygamous None Protandrous None Protogynous None Subandroecious None Subdioecious None Subgynoecious None Synoecious None Trimonoecious None Trioecious None Unisexual None"},{"location":"PlantSexEnum/#slots","title":"Slots","text":"Name Description plant_sex Sex of the reproductive parts on the whole plant, e"},{"location":"PlantSexEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PlantSexEnum/#schema-source","title":"Schema Source","text":"name: plant_sex_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Androdioecious:\n text: Androdioecious\n Androecious:\n text: Androecious\n Androgynous:\n text: Androgynous\n Androgynomonoecious:\n text: Androgynomonoecious\n Andromonoecious:\n text: Andromonoecious\n Bisexual:\n text: Bisexual\n Dichogamous:\n text: Dichogamous\n Diclinous:\n text: Diclinous\n Dioecious:\n text: Dioecious\n Gynodioecious:\n text: Gynodioecious\n Gynoecious:\n text: Gynoecious\n Gynomonoecious:\n text: Gynomonoecious\n Hermaphroditic:\n text: Hermaphroditic\n Imperfect:\n text: Imperfect\n Monoclinous:\n text: Monoclinous\n Monoecious:\n text: Monoecious\n Perfect:\n text: Perfect\n Polygamodioecious:\n text: Polygamodioecious\n Polygamomonoecious:\n text: Polygamomonoecious\n Polygamous:\n text: Polygamous\n Protandrous:\n text: Protandrous\n Protogynous:\n text: Protogynous\n Subandroecious:\n text: Subandroecious\n Subdioecious:\n text: Subdioecious\n Subgynoecious:\n text: Subgynoecious\n Synoecious:\n text: Synoecious\n Trimonoecious:\n text: Trimonoecious\n Trioecious:\n text: Trioecious\n Unisexual:\n text: Unisexual\n\nURI: PolarityModeEnum
"},{"location":"PolarityModeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description positive None negative None"},{"location":"PolarityModeEnum/#slots","title":"Slots","text":"Name Description polarity_mode the polarity of which ions are generated and detected"},{"location":"PolarityModeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"PolarityModeEnum/#schema-source","title":"Schema Source","text":"name: PolarityModeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n positive:\n text: positive\n negative:\n text: negative\n\nphysical combination of several instances of like material.
URI: nmdc:Pooling
classDiagram\n class Pooling\n click Pooling href \"../Pooling\"\n MaterialProcessing <|-- Pooling\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n Pooling : alternative_identifiers\n\n Pooling : description\n\n Pooling : end_date\n\n Pooling : has_failure_categorization\n\n Pooling --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n Pooling : has_input\n\n Pooling --> \"1..*\" Sample : has_input\n click Sample href \"../Sample\"\n\n Pooling : has_output\n\n Pooling --> \"1..*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n Pooling : id\n\n Pooling : instrument_used\n\n Pooling --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n Pooling : name\n\n Pooling : processing_institution\n\n Pooling --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n Pooling : protocol_link\n\n Pooling --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n Pooling : qc_comment\n\n Pooling : qc_status\n\n Pooling --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n Pooling : start_date\n\n Pooling : type\n\n\n\nname: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: MaterialProcessing\nslot_usage:\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 2\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 1\n maximum_cardinality: 1\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:Pooling\n\nname: Pooling\ndescription: physical combination of several instances of like material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0600016\nis_a: MaterialProcessing\nslot_usage:\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 2\n has_output:\n name: has_output\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 1\n maximum_cardinality: 1\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: Pooling\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: Sample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 2\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n minimum_cardinality: 1\n maximum_cardinality: 1\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Pooling\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: Pooling\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Pooling\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:poolp-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Pooling\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Pooling\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Pooling\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Pooling\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Pooling\n\nA portion of any matter of defined composition that has discrete existence, whose origin may be biological, mineral or chemical.
URI: nmdc:PortionOfSubstance
classDiagram\n class PortionOfSubstance\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n PortionOfSubstance : final_concentration\n\n PortionOfSubstance --> \"0..1\" QuantityValue : final_concentration\n click QuantityValue href \"../QuantityValue\"\n\n PortionOfSubstance : known_as\n\n PortionOfSubstance --> \"0..1\" ChemicalEntityEnum : known_as\n click ChemicalEntityEnum href \"../ChemicalEntityEnum\"\n\n PortionOfSubstance : mass\n\n PortionOfSubstance --> \"0..1\" QuantityValue : mass\n click QuantityValue href \"../QuantityValue\"\n\n PortionOfSubstance : sample_state_information\n\n PortionOfSubstance --> \"0..1\" SampleStateEnum : sample_state_information\n click SampleStateEnum href \"../SampleStateEnum\"\n\n PortionOfSubstance : source_concentration\n\n PortionOfSubstance --> \"0..1\" QuantityValue : source_concentration\n click QuantityValue href \"../QuantityValue\"\n\n PortionOfSubstance : substance_role\n\n PortionOfSubstance --> \"0..1\" SubstanceRoleEnum : substance_role\n click SubstanceRoleEnum href \"../SubstanceRoleEnum\"\n\n PortionOfSubstance : type\n\n PortionOfSubstance : volume\n\n PortionOfSubstance --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: PortionOfSubstance\ndescription: A portion of any matter of defined composition that has discrete existence,\n whose origin may be biological, mineral or chemical.\ntitle: Portion of a Substance\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:Substance\nslots:\n- final_concentration\n- mass\n- sample_state_information\n- source_concentration\n- known_as\n- substance_role\n- type\n- volume\nclass_uri: nmdc:PortionOfSubstance\n\nname: PortionOfSubstance\ndescription: A portion of any matter of defined composition that has discrete existence,\n whose origin may be biological, mineral or chemical.\ntitle: Portion of a Substance\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:Substance\nattributes:\n final_concentration:\n name: final_concentration\n description: When solutions A (containing substance X) and B are combined together,\n this slot captures the concentration of X in the combination\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: concentration\n alias: final_concentration\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: QuantityValue\n mass:\n name: mass\n description: A physical quality that inheres in a bearer by virtue of the proportion\n of the bearer's amount of matter.\n title: mass\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - PATO:0000125\n rank: 1000\n alias: mass\n owner: PortionOfSubstance\n domain_of:\n - SubSamplingProcess\n - PortionOfSubstance\n range: QuantityValue\n sample_state_information:\n name: sample_state_information\n description: The chemical phase of a pure sample, or the state of a mixed sample\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sample_state_information\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: SampleStateEnum\n source_concentration:\n name: source_concentration\n description: When solutions A (containing substance X) and B are combined together,\n this slot captures the concentration of X in solution A\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: concentration\n alias: source_concentration\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: QuantityValue\n known_as:\n name: known_as\n description: The substance from which a portion was taken.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: known_as\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: ChemicalEntityEnum\n substance_role:\n name: substance_role\n description: The role of a substance in a process\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substance_role\n owner: PortionOfSubstance\n domain_of:\n - PortionOfSubstance\n range: SubstanceRoleEnum\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: PortionOfSubstance\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\n volume:\n name: volume\n description: The volume of a substance.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: PortionOfSubstance\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\nclass_uri: nmdc:PortionOfSubstance\n\nURI: nmdc:ProcessedSample
classDiagram\n class ProcessedSample\n click ProcessedSample href \"../ProcessedSample\"\n Sample <|-- ProcessedSample\n click Sample href \"../Sample\"\n\n\n\n ProcessedSample : alternative_identifiers\n\n ProcessedSample : biomaterial_purity\n\n ProcessedSample --> \"0..1\" QuantityValue : biomaterial_purity\n click QuantityValue href \"../QuantityValue\"\n\n ProcessedSample : description\n\n ProcessedSample : dna_absorb1\n\n ProcessedSample : dna_concentration\n\n ProcessedSample : external_database_identifiers\n\n ProcessedSample : id\n\n ProcessedSample : name\n\n ProcessedSample : type\n\n\n\nname: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Sample\nslots:\n- biomaterial_purity\n- dna_absorb1\n- dna_concentration\n- external_database_identifiers\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ProcessedSample\n\nname: ProcessedSample\ntitle: Processed Sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: Sample\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n biomaterial_purity:\n name: biomaterial_purity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: biomaterial_purity\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: QuantityValue\n dna_absorb1:\n name: dna_absorb1\n description: 260/280 measurement of DNA sample purity\n title: DNA absorbance 260/280\n comments:\n - Recommended value is between 1 and 3.\n examples:\n - value: '2.02'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 7\n is_a: biomaterial_purity\n alias: dna_absorb1\n owner: ProcessedSample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n dna_concentration:\n name: dna_concentration\n title: DNA concentration in ng/ul\n comments:\n - Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\n examples:\n - value: '100'\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:nucleic_acid_concentration\n rank: 5\n alias: dna_concentration\n owner: ProcessedSample\n domain_of:\n - Biosample\n - ProcessedSample\n slot_group: JGI-Metagenomics\n range: float\n recommended: true\n minimum_value: 0\n maximum_value: 2000\n external_database_identifiers:\n name: external_database_identifiers\n description: Link to corresponding identifier in external database\n notes:\n - had tried ranges of external identifier and string\n comments:\n - The value of this field is always a registered CURIE\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - skos:closeMatch\n rank: 1000\n is_a: alternative_identifiers\n abstract: true\n alias: external_database_identifiers\n owner: ProcessedSample\n domain_of:\n - ProcessedSample\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ProcessedSample\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ProcessedSample\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ProcessedSample\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ProcessedSample\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ProcessedSample\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ProcessedSample\n\nURI: ProcessingInstitutionEnum
"},{"location":"ProcessingInstitutionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description UCSD https://ror.org/0168r3w48 JGI https://ror.org/04xm1d337 EMSL https://ror.org/04rc0xn13 Battelle https://ror.org/01h5tnr73 ANL https://ror.org/05gvnxz63 UCD_Genome_Center https://genomecenter.ucdavis.edu/ Azenta https://www.azenta.com/"},{"location":"ProcessingInstitutionEnum/#slots","title":"Slots","text":"Name Description processing_institution The organization that processed the sample"},{"location":"ProcessingInstitutionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProcessingInstitutionEnum/#schema-source","title":"Schema Source","text":"name: ProcessingInstitutionEnum\nnotes:\n- use ROR meanings like https://ror.org/0168r3w48 for UCSD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n UCSD:\n text: UCSD\n meaning: https://ror.org/0168r3w48\n title: University of California, San Diego\n JGI:\n text: JGI\n meaning: https://ror.org/04xm1d337\n title: Joint Genome Institute\n EMSL:\n text: EMSL\n meaning: https://ror.org/04rc0xn13\n title: Environmental Molecular Sciences Laboratory\n aliases:\n - Environmental Molecular Science Laboratory\n - Environmental Molecular Sciences Lab\n Battelle:\n text: Battelle\n meaning: https://ror.org/01h5tnr73\n title: Battelle Memorial Institute\n ANL:\n text: ANL\n meaning: https://ror.org/05gvnxz63\n title: Argonne National Laboratory\n UCD_Genome_Center:\n text: UCD_Genome_Center\n meaning: https://genomecenter.ucdavis.edu/\n title: University of California, Davis Genome Center\n Azenta:\n text: Azenta\n meaning: https://www.azenta.com/\n title: Azenta Life Sciences\n\nURI: ProfilePositionEnum
"},{"location":"ProfilePositionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description summit None shoulder None backslope None footslope None toeslope None"},{"location":"ProfilePositionEnum/#slots","title":"Slots","text":"Name Description profile_position Cross-sectional position in the hillslope where sample was collected"},{"location":"ProfilePositionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProfilePositionEnum/#schema-source","title":"Schema Source","text":"name: profile_position_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n summit:\n text: summit\n shoulder:\n text: shoulder\n backslope:\n text: backslope\n footslope:\n text: footslope\n toeslope:\n text: toeslope\n\nThis is used to link a metaproteomics analysis workflow to a specific protein
URI: nmdc:ProteinQuantification
classDiagram\n class ProteinQuantification\n click ProteinQuantification href \"../ProteinQuantification\"\n\n ProteinQuantification : all_proteins\n\n ProteinQuantification --> \"*\" GeneProduct : all_proteins\n click GeneProduct href \"../GeneProduct\"\n\n ProteinQuantification : best_protein\n\n ProteinQuantification --> \"0..1\" GeneProduct : best_protein\n click GeneProduct href \"../GeneProduct\"\n\n ProteinQuantification : peptide_sequence_count\n\n ProteinQuantification : protein_spectral_count\n\n ProteinQuantification : protein_sum_masic_abundance\n\n ProteinQuantification : type\n\n\n\nname: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n protein\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- all_proteins\n- best_protein\n- peptide_sequence_count\n- protein_spectral_count\n- protein_sum_masic_abundance\n- type\nclass_uri: nmdc:ProteinQuantification\n\nname: ProteinQuantification\ndescription: This is used to link a metaproteomics analysis workflow to a specific\n protein\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n all_proteins:\n name: all_proteins\n description: the list of protein identifiers that are associated with the peptide\n sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: all_proteins\n owner: ProteinQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n multivalued: true\n best_protein:\n name: best_protein\n description: the specific protein identifier most correctly associated with the\n peptide sequence\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: best_protein\n owner: ProteinQuantification\n domain_of:\n - PeptideQuantification\n - ProteinQuantification\n range: GeneProduct\n peptide_sequence_count:\n name: peptide_sequence_count\n description: count of peptide sequences grouped to the best_protein\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: peptide_sequence_count\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n protein_spectral_count:\n name: protein_spectral_count\n description: sum of filter passing MS2 spectra associated with the best protein\n within a given LC-MS/MS data file\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protein_spectral_count\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n protein_sum_masic_abundance:\n name: protein_sum_masic_abundance\n description: combined MS1 extracted ion chromatograms derived from MS2 spectra\n associated with the best protein from a given LC-MS/MS data file using the MASIC\n tool\n deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protein_sum_masic_abundance\n owner: ProteinQuantification\n domain_of:\n - ProteinQuantification\n range: integer\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ProteinQuantification\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ProteinQuantification\n\nURI: nmdc:Protocol
classDiagram\n class Protocol\n click Protocol href \"../Protocol\"\n\n Protocol : name\n\n Protocol : type\n\n Protocol : url\n\n\n\nname: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nslots:\n- url\n- name\n- type\nclass_uri: nmdc:Protocol\n\nname: Protocol\nfrom_schema: https://w3id.org/nmdc/nmdc\nattributes:\n url:\n name: url\n notes:\n - See issue 207 - this clashes with the mixs field\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: url\n owner: Protocol\n domain_of:\n - ImageValue\n - Protocol\n - DataObject\n range: string\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Protocol\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Protocol\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Protocol\n\nThe possible protocols that may be followed for an assay.
URI: ProtocolCategoryEnum
"},{"location":"ProtocolCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description mplex None derivatization None filter_clean_up None organic_matter_extraction None solid_phase_extraction None phosphorus_extraction None ph_measurement None respiration_measurement None texture_measurement None dna_extraction None phenol_chloroform_extraction None"},{"location":"ProtocolCategoryEnum/#slots","title":"Slots","text":"Name Description protocol_execution_category"},{"location":"ProtocolCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ProtocolCategoryEnum/#schema-source","title":"Schema Source","text":"name: ProtocolCategoryEnum\ndescription: The possible protocols that may be followed for an assay.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n mplex:\n text: mplex\n derivatization:\n text: derivatization\n filter_clean_up:\n text: filter_clean_up\n organic_matter_extraction:\n text: organic_matter_extraction\n solid_phase_extraction:\n text: solid_phase_extraction\n phosphorus_extraction:\n text: phosphorus_extraction\n ph_measurement:\n text: ph_measurement\n respiration_measurement:\n text: respiration_measurement\n texture_measurement:\n text: texture_measurement\n dna_extraction:\n text: dna_extraction\n phenol_chloroform_extraction:\n text: phenol_chloroform_extraction\n\nA PlannedProces that has PlannedProcess parts. Can be used to represent the case of someone following a Protocol.
URI: nmdc:ProtocolExecution
classDiagram\n class ProtocolExecution\n click ProtocolExecution href \"../ProtocolExecution\"\n PlannedProcess <|-- ProtocolExecution\n click PlannedProcess href \"../PlannedProcess\"\n\n\n\n ProtocolExecution : alternative_identifiers\n\n ProtocolExecution : description\n\n ProtocolExecution : end_date\n\n ProtocolExecution : has_failure_categorization\n\n ProtocolExecution --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ProtocolExecution : has_input\n\n ProtocolExecution --> \"*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n ProtocolExecution : has_output\n\n ProtocolExecution --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n ProtocolExecution : has_process_parts\n\n ProtocolExecution --> \"1..*\" PlannedProcess : has_process_parts\n click PlannedProcess href \"../PlannedProcess\"\n\n ProtocolExecution : id\n\n ProtocolExecution : name\n\n ProtocolExecution : processing_institution\n\n ProtocolExecution --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ProtocolExecution : protocol_execution_category\n\n ProtocolExecution --> \"1\" ProtocolCategoryEnum : protocol_execution_category\n click ProtocolCategoryEnum href \"../ProtocolCategoryEnum\"\n\n ProtocolExecution : protocol_link\n\n ProtocolExecution --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ProtocolExecution : qc_comment\n\n ProtocolExecution : qc_status\n\n ProtocolExecution --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ProtocolExecution : start_date\n\n ProtocolExecution : type\n\n\n\nname: ProtocolExecution\ndescription: A PlannedProces that has PlannedProcess parts. Can be used to represent\n the case of someone following a Protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: PlannedProcess\nslots:\n- has_process_parts\n- protocol_execution_category\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_process_parts:\n name: has_process_parts\n description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ProtocolExecution\n\nname: ProtocolExecution\ndescription: A PlannedProces that has PlannedProcess parts. Can be used to represent\n the case of someone following a Protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: PlannedProcess\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_process_parts:\n name: has_process_parts\n description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n has_process_parts:\n name: has_process_parts\n description: The MaterialProcessing steps that are discrete parts of the ProtocolExecution.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n list_elements_ordered: true\n alias: has_process_parts\n owner: ProtocolExecution\n domain_of:\n - ProtocolExecution\n range: PlannedProcess\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(extrp|filtpr|dispro|poolp|libprp|subspr|mixpro|chcpr|cspro)-{id_shoulder}-{id_blade}$'\n interpolated: true\n protocol_execution_category:\n name: protocol_execution_category\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_execution_category\n owner: ProtocolExecution\n domain_of:\n - ProtocolExecution\n range: ProtocolCategoryEnum\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ProtocolExecution\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ProtocolExecution\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:pex-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ProtocolExecution\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ProtocolExecution\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ProtocolExecution\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ProtocolExecution\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ProtocolExecution\n\nURI: QuadPosEnum
"},{"location":"QuadPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description North side None West side None South side None East side None"},{"location":"QuadPosEnum/#slots","title":"Slots","text":"Name Description quad_pos The quadrant position of the sampling room within the building"},{"location":"QuadPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"QuadPosEnum/#schema-source","title":"Schema Source","text":"name: quad_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n North side:\n text: North side\n West side:\n text: West side\n South side:\n text: South side\n East side:\n text: East side\n\nA simple quantity, e.g. 2cm
URI: nmdc:QuantityValue
classDiagram\n class QuantityValue\n click QuantityValue href \"../QuantityValue\"\n AttributeValue <|-- QuantityValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n QuantityValue : has_maximum_numeric_value\n\n QuantityValue : has_minimum_numeric_value\n\n QuantityValue : has_numeric_value\n\n QuantityValue : has_raw_value\n\n QuantityValue : has_unit\n\n QuantityValue : type\n\n\n\nname: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslots:\n- has_maximum_numeric_value\n- has_minimum_numeric_value\n- has_numeric_value\n- has_unit\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n has_unit:\n name: has_unit\n description: The unit of the quantity\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\nclass_uri: nmdc:QuantityValue\n\nname: QuantityValue\ndescription: A simple quantity, e.g. 2cm\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:QuantityValue\nis_a: AttributeValue\nslot_usage:\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n has_unit:\n name: has_unit\n description: The unit of the quantity\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\nattributes:\n has_maximum_numeric_value:\n name: has_maximum_numeric_value\n description: The maximum value part, expressed as number, of the quantity value\n when the value covers a range.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_numeric_value\n alias: has_maximum_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: decimal\n has_minimum_numeric_value:\n name: has_minimum_numeric_value\n description: The minimum value part, expressed as number, of the quantity value\n when the value covers a range.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: has_numeric_value\n alias: has_minimum_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: decimal\n has_numeric_value:\n name: has_numeric_value\n description: The number part of the quantity\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - qud:quantityValue\n - schema:value\n rank: 1000\n alias: has_numeric_value\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: decimal\n has_unit:\n name: has_unit\n description: The unit of the quantity\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - scale\n mappings:\n - qud:unit\n - schema:unitCode\n rank: 1000\n alias: has_unit\n owner: QuantityValue\n domain_of:\n - QuantityValue\n range: unit\n has_raw_value:\n name: has_raw_value\n description: Unnormalized atomic string representation, should in syntax {number}\n {unit}\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: QuantityValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: QuantityValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:QuantityValue\n\nURI: RNASampleFormatEnum
"},{"location":"RNASampleFormatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 10 mM Tris-HCl None DNAStable None Ethanol None Low EDTA TE None MDA reaction buffer None PBS None Pellet None RNAStable None TE None Water None Gentegra-DNA None Gentegra-RNA None"},{"location":"RNASampleFormatEnum/#slots","title":"Slots","text":"Name Description rna_sample_format Solution in which the RNA sample has been suspended"},{"location":"RNASampleFormatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RNASampleFormatEnum/#schema-source","title":"Schema Source","text":"name: RNASampleFormatEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 10 mM Tris-HCl:\n text: 10 mM Tris-HCl\n DNAStable:\n text: DNAStable\n Ethanol:\n text: Ethanol\n Low EDTA TE:\n text: Low EDTA TE\n MDA reaction buffer:\n text: MDA reaction buffer\n PBS:\n text: PBS\n Pellet:\n text: Pellet\n RNAStable:\n text: RNAStable\n TE:\n text: TE\n Water:\n text: Water\n Gentegra-DNA:\n text: Gentegra-DNA\n Gentegra-RNA:\n text: Gentegra-RNA\n\nA workflow execution activity that performs taxonomy classification using sequencing reads
URI: nmdc:ReadBasedTaxonomyAnalysis
classDiagram\n class ReadBasedTaxonomyAnalysis\n click ReadBasedTaxonomyAnalysis href \"../ReadBasedTaxonomyAnalysis\"\n WorkflowExecution <|-- ReadBasedTaxonomyAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n ReadBasedTaxonomyAnalysis : alternative_identifiers\n\n ReadBasedTaxonomyAnalysis : description\n\n ReadBasedTaxonomyAnalysis : end_date\n\n ReadBasedTaxonomyAnalysis : ended_at_time\n\n ReadBasedTaxonomyAnalysis : execution_resource\n\n ReadBasedTaxonomyAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n ReadBasedTaxonomyAnalysis : git_url\n\n ReadBasedTaxonomyAnalysis : has_failure_categorization\n\n ReadBasedTaxonomyAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ReadBasedTaxonomyAnalysis : has_input\n\n ReadBasedTaxonomyAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n ReadBasedTaxonomyAnalysis : has_output\n\n ReadBasedTaxonomyAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n ReadBasedTaxonomyAnalysis : id\n\n ReadBasedTaxonomyAnalysis : name\n\n ReadBasedTaxonomyAnalysis : processing_institution\n\n ReadBasedTaxonomyAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ReadBasedTaxonomyAnalysis : protocol_link\n\n ReadBasedTaxonomyAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ReadBasedTaxonomyAnalysis : qc_comment\n\n ReadBasedTaxonomyAnalysis : qc_status\n\n ReadBasedTaxonomyAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ReadBasedTaxonomyAnalysis : start_date\n\n ReadBasedTaxonomyAnalysis : started_at_time\n\n ReadBasedTaxonomyAnalysis : type\n\n ReadBasedTaxonomyAnalysis : version\n\n ReadBasedTaxonomyAnalysis : was_informed_by\n\n ReadBasedTaxonomyAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: ReadBasedTaxonomyAnalysis\ndescription: A workflow execution activity that performs taxonomy classification using\n sequencing reads\ntitle: Read based analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ReadBasedTaxonomyAnalysis\n\nname: ReadBasedTaxonomyAnalysis\ndescription: A workflow execution activity that performs taxonomy classification using\n sequencing reads\ntitle: Read based analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrbt-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ReadBasedTaxonomyAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ReadBasedTaxonomyAnalysis\n\nA workflow execution activity that performs quality control on raw Illumina reads including quality trimming, artifact removal, linker trimming, adapter trimming, spike-in removal, and human/cat/dog/mouse/microbe contaminant removal
URI: nmdc:ReadQcAnalysis
classDiagram\n class ReadQcAnalysis\n click ReadQcAnalysis href \"../ReadQcAnalysis\"\n WorkflowExecution <|-- ReadQcAnalysis\n click WorkflowExecution href \"../WorkflowExecution\"\n\n\n\n ReadQcAnalysis : alternative_identifiers\n\n ReadQcAnalysis : description\n\n ReadQcAnalysis : end_date\n\n ReadQcAnalysis : ended_at_time\n\n ReadQcAnalysis : execution_resource\n\n ReadQcAnalysis --> \"1\" ExecutionResourceEnum : execution_resource\n click ExecutionResourceEnum href \"../ExecutionResourceEnum\"\n\n ReadQcAnalysis : git_url\n\n ReadQcAnalysis : has_failure_categorization\n\n ReadQcAnalysis --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n ReadQcAnalysis : has_input\n\n ReadQcAnalysis --> \"1..*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n ReadQcAnalysis : has_output\n\n ReadQcAnalysis --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n ReadQcAnalysis : id\n\n ReadQcAnalysis : input_base_count\n\n ReadQcAnalysis : input_read_bases\n\n ReadQcAnalysis : input_read_count\n\n ReadQcAnalysis : name\n\n ReadQcAnalysis : output_base_count\n\n ReadQcAnalysis : output_read_bases\n\n ReadQcAnalysis : output_read_count\n\n ReadQcAnalysis : processing_institution\n\n ReadQcAnalysis --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n ReadQcAnalysis : protocol_link\n\n ReadQcAnalysis --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n ReadQcAnalysis : qc_comment\n\n ReadQcAnalysis : qc_status\n\n ReadQcAnalysis --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n ReadQcAnalysis : start_date\n\n ReadQcAnalysis : started_at_time\n\n ReadQcAnalysis : type\n\n ReadQcAnalysis : version\n\n ReadQcAnalysis : was_informed_by\n\n ReadQcAnalysis --> \"1\" DataGeneration : was_informed_by\n click DataGeneration href \"../DataGeneration\"\n\n\n\nname: ReadQcAnalysis\ndescription: A workflow execution activity that performs quality control on raw Illumina\n reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslots:\n- input_base_count\n- input_read_bases\n- input_read_count\n- output_base_count\n- output_read_bases\n- output_read_count\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:ReadQcAnalysis\n\nname: ReadQcAnalysis\ndescription: A workflow execution activity that performs quality control on raw Illumina\n reads including quality trimming, artifact removal, linker trimming, adapter trimming,\n spike-in removal, and human/cat/dog/mouse/microbe contaminant removal\ntitle: Read quality control analysis activity\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: WorkflowExecution\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n was_informed_by:\n name: was_informed_by\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n input_base_count:\n name: input_base_count\n description: The nucleotide base count number of input reads for QC analysis.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: input_base_count\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n input_read_bases:\n name: input_read_bases\n description: 'TODO '\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: input_read_bases\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n input_read_count:\n name: input_read_count\n description: The sequence count number of input reads for QC analysis.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: input_read_count\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n output_base_count:\n name: output_base_count\n description: After QC analysis nucleotide base count number.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: output_base_count\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n output_read_bases:\n name: output_read_bases\n description: TODO\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: output_read_bases\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n output_read_count:\n name: output_read_count\n description: After QC analysis sequence count number.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: read_qc_analysis_statistic\n alias: output_read_count\n owner: ReadQcAnalysis\n domain_of:\n - ReadQcAnalysis\n range: float\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: ReadQcAnalysis\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(omprc|dgns)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: ReadQcAnalysis\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: ReadQcAnalysis\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:wfrqc-{id_shoulder}-{id_blade}{id_version}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: ReadQcAnalysis\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: ReadQcAnalysis\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: ReadQcAnalysis\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: ReadQcAnalysis\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:ReadQcAnalysis\n\nURI: RelSampLocEnum
"},{"location":"RelSampLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description edge of car None center of car None under a seat None"},{"location":"RelSampLocEnum/#slots","title":"Slots","text":"Name Description rel_samp_loc The sampling location within the train car"},{"location":"RelSampLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RelSampLocEnum/#schema-source","title":"Schema Source","text":"name: rel_samp_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n edge of car:\n text: edge of car\n center of car:\n text: center of car\n under a seat:\n text: under a seat\n\nURI: ResolutionCategoryEnum
"},{"location":"ResolutionCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description high None higher than unit resolution low None at unit resolution"},{"location":"ResolutionCategoryEnum/#slots","title":"Slots","text":"Name Description resolution_categories The relative resolution at which spectra were collected"},{"location":"ResolutionCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ResolutionCategoryEnum/#schema-source","title":"Schema Source","text":"name: ResolutionCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n high:\n text: high\n description: higher than unit resolution\n low:\n text: low\n description: at unit resolution\n\nURI: RoomCondtEnum
"},{"location":"RoomCondtEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description new None visible wear None needs repair None damaged None rupture None visible signs of mold/mildew None"},{"location":"RoomCondtEnum/#slots","title":"Slots","text":"Name Description room_condt The condition of the room at the time of sampling"},{"location":"RoomCondtEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomCondtEnum/#schema-source","title":"Schema Source","text":"name: room_condt_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n new:\n text: new\n visible wear:\n text: visible wear\n needs repair:\n text: needs repair\n damaged:\n text: damaged\n rupture:\n text: rupture\n visible signs of mold/mildew:\n text: visible signs of mold/mildew\n\nURI: RoomConnectedEnum
"},{"location":"RoomConnectedEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None office None stairwell None"},{"location":"RoomConnectedEnum/#slots","title":"Slots","text":"Name Description room_connected List of rooms connected to the sampling room by a doorway"},{"location":"RoomConnectedEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomConnectedEnum/#schema-source","title":"Schema Source","text":"name: room_connected_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n attic:\n text: attic\n bathroom:\n text: bathroom\n closet:\n text: closet\n conference room:\n text: conference room\n elevator:\n text: elevator\n examining room:\n text: examining room\n hallway:\n text: hallway\n kitchen:\n text: kitchen\n mail room:\n text: mail room\n office:\n text: office\n stairwell:\n text: stairwell\n\nURI: RoomLocEnum
"},{"location":"RoomLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description corner room None interior room None exterior wall None"},{"location":"RoomLocEnum/#slots","title":"Slots","text":"Name Description room_loc The position of the room within the building"},{"location":"RoomLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomLocEnum/#schema-source","title":"Schema Source","text":"name: room_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n corner room:\n text: corner room\n interior room:\n text: interior room\n exterior wall:\n text: exterior wall\n\nURI: RoomSampPosEnum
"},{"location":"RoomSampPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north corner None south corner None west corner None east corner None northeast corner None northwest corner None southeast corner None southwest corner None center None"},{"location":"RoomSampPosEnum/#slots","title":"Slots","text":"Name Description room_samp_pos The horizontal sampling position in the room relative to architectural elemen..."},{"location":"RoomSampPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomSampPosEnum/#schema-source","title":"Schema Source","text":"name: room_samp_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north corner:\n text: north corner\n south corner:\n text: south corner\n west corner:\n text: west corner\n east corner:\n text: east corner\n northeast corner:\n text: northeast corner\n northwest corner:\n text: northwest corner\n southeast corner:\n text: southeast corner\n southwest corner:\n text: southwest corner\n center:\n text: center\n\nURI: RoomTypeEnum
"},{"location":"RoomTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description attic None bathroom None closet None conference room None elevator None examining room None hallway None kitchen None mail room None private office None open office None stairwell None ,restroom None lobby None vestibule None mechanical or electrical room None data center None laboratory_wet None laboratory_dry None gymnasium None natatorium None auditorium None lockers None cafe None warehouse None"},{"location":"RoomTypeEnum/#slots","title":"Slots","text":"Name Description room_type The main purpose or activity of the sampling room"},{"location":"RoomTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"RoomTypeEnum/#schema-source","title":"Schema Source","text":"name: room_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n attic:\n text: attic\n bathroom:\n text: bathroom\n closet:\n text: closet\n conference room:\n text: conference room\n elevator:\n text: elevator\n examining room:\n text: examining room\n hallway:\n text: hallway\n kitchen:\n text: kitchen\n mail room:\n text: mail room\n private office:\n text: private office\n open office:\n text: open office\n stairwell:\n text: stairwell\n ',restroom':\n text: ',restroom'\n lobby:\n text: lobby\n vestibule:\n text: vestibule\n mechanical or electrical room:\n text: mechanical or electrical room\n data center:\n text: data center\n laboratory_wet:\n text: laboratory_wet\n laboratory_dry:\n text: laboratory_dry\n gymnasium:\n text: gymnasium\n natatorium:\n text: natatorium\n auditorium:\n text: auditorium\n lockers:\n text: lockers\n cafe:\n text: cafe\n warehouse:\n text: warehouse\n\nURI: SampCaptStatusEnum
"},{"location":"SampCaptStatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description active surveillance in response to an outbreak None active surveillance not initiated by an outbreak None farm sample None market sample None other None"},{"location":"SampCaptStatusEnum/#slots","title":"Slots","text":"Name Description samp_capt_status Reason for the sample"},{"location":"SampCaptStatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCaptStatusEnum/#schema-source","title":"Schema Source","text":"name: samp_capt_status_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n active surveillance in response to an outbreak:\n text: active surveillance in response to an outbreak\n active surveillance not initiated by an outbreak:\n text: active surveillance not initiated by an outbreak\n farm sample:\n text: farm sample\n market sample:\n text: market sample\n other:\n text: other\n\nURI: SampCollectPointEnum
"},{"location":"SampCollectPointEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description well None test well None drilling rig None wellhead None separator None storage tank None other None"},{"location":"SampCollectPointEnum/#slots","title":"Slots","text":"Name Description samp_collect_point Sampling point on the asset were sample was collected (e"},{"location":"SampCollectPointEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampCollectPointEnum/#schema-source","title":"Schema Source","text":"name: samp_collect_point_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n well:\n text: well\n test well:\n text: test well\n drilling rig:\n text: drilling rig\n wellhead:\n text: wellhead\n separator:\n text: separator\n storage tank:\n text: storage tank\n other:\n text: other\n\nURI: SampDisStageEnum
"},{"location":"SampDisStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dissemination None growth and reproduction None infection None inoculation None penetration None other None"},{"location":"SampDisStageEnum/#slots","title":"Slots","text":"Name Description samp_dis_stage Stage of the disease at the time of sample collection, e"},{"location":"SampDisStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampDisStageEnum/#schema-source","title":"Schema Source","text":"name: samp_dis_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n dissemination:\n text: dissemination\n growth and reproduction:\n text: growth and reproduction\n infection:\n text: infection\n inoculation:\n text: inoculation\n penetration:\n text: penetration\n other:\n text: other\n\nURI: SampFloorEnum
"},{"location":"SampFloorEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 1st floor None 2nd floor None basement None lobby None"},{"location":"SampFloorEnum/#slots","title":"Slots","text":"Name Description samp_floor The floor of the building, where the sampling room is located"},{"location":"SampFloorEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampFloorEnum/#schema-source","title":"Schema Source","text":"name: samp_floor_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 1st floor:\n text: 1st floor\n 2nd floor:\n text: 2nd floor\n basement:\n text: basement\n lobby:\n text: lobby\n\nURI: SampMdEnum
"},{"location":"SampMdEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description DF None RT None KB None MSL None other None"},{"location":"SampMdEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampMdEnum/#schema-source","title":"Schema Source","text":"name: samp_md_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n DF:\n text: DF\n RT:\n text: RT\n KB:\n text: KB\n MSL:\n text: MSL\n other:\n text: other\n\nURI: SampSubtypeEnum
"},{"location":"SampSubtypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description oil phase None water phase None biofilm None not applicable None other None"},{"location":"SampSubtypeEnum/#slots","title":"Slots","text":"Name Description samp_subtype Name of sample sub-type"},{"location":"SampSubtypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampSubtypeEnum/#schema-source","title":"Schema Source","text":"name: samp_subtype_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n oil phase:\n text: oil phase\n water phase:\n text: water phase\n biofilm:\n text: biofilm\n not applicable:\n text: not applicable\n other:\n text: other\n\nURI: SampWeatherEnum
"},{"location":"SampWeatherEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clear sky None cloudy None foggy None hail None rain None snow None sleet None sunny None windy None"},{"location":"SampWeatherEnum/#slots","title":"Slots","text":"Name Description samp_weather The weather on the sampling day"},{"location":"SampWeatherEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampWeatherEnum/#schema-source","title":"Schema Source","text":"name: samp_weather_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n clear sky:\n text: clear sky\n cloudy:\n text: cloudy\n foggy:\n text: foggy\n hail:\n text: hail\n rain:\n text: rain\n snow:\n text: snow\n sleet:\n text: sleet\n sunny:\n text: sunny\n windy:\n text: windy\n\nA sample is a material entity that can be characterized by an experiment.
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:Sample
classDiagram\n class Sample\n click Sample href \"../Sample\"\n MaterialEntity <|-- Sample\n click MaterialEntity href \"../MaterialEntity\"\n\n\n Sample <|-- Biosample\n click Biosample href \"../Biosample\"\n Sample <|-- ProcessedSample\n click ProcessedSample href \"../ProcessedSample\"\n\n\n\n Sample : alternative_identifiers\n\n Sample : description\n\n Sample : id\n\n Sample : name\n\n Sample : type\n\n\n\nname: Sample\ndescription: A sample is a material entity that can be characterized by an experiment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nclass_uri: nmdc:Sample\n\nname: Sample\ndescription: A sample is a material entity that can be characterized by an experiment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Sample\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Sample\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Sample\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Sample\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Sample\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Sample\n\nURI: SamplePortionEnum
"},{"location":"SamplePortionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description supernatant None pellet None organic_layer None aqueous_layer None non_polar_layer None"},{"location":"SamplePortionEnum/#slots","title":"Slots","text":"Name Description sampled_portion The portion of the sample that is taken for downstream activity"},{"location":"SamplePortionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SamplePortionEnum/#schema-source","title":"Schema Source","text":"name: SamplePortionEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n supernatant:\n text: supernatant\n aliases:\n - top_layer\n pellet:\n text: pellet\n aliases:\n - bottom_layer\n organic_layer:\n text: organic_layer\n aqueous_layer:\n text: aqueous_layer\n non_polar_layer:\n text: non_polar_layer\n\nURI: SampleStateEnum
"},{"location":"SampleStateEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description solid None liquid None gas None"},{"location":"SampleStateEnum/#slots","title":"Slots","text":"Name Description sample_state_information The chemical phase of a pure sample, or the state of a mixed sample"},{"location":"SampleStateEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleStateEnum/#schema-source","title":"Schema Source","text":"name: SampleStateEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n solid:\n text: solid\n liquid:\n text: liquid\n gas:\n text: gas\n\nURI: SampleTypeEnum
"},{"location":"SampleTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description soil None soil - water extract None plant associated None sediment None water None"},{"location":"SampleTypeEnum/#slots","title":"Slots","text":"Name Description sample_type Type of sample being submitted"},{"location":"SampleTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SampleTypeEnum/#schema-source","title":"Schema Source","text":"name: SampleTypeEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n soil:\n text: soil\n soil - water extract:\n text: soil - water extract\n plant associated:\n text: plant associated\n sediment:\n text: sediment\n water:\n text: water\n\nURI: SeasonUseEnum
"},{"location":"SeasonUseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Spring None Summer None Fall None Winter None"},{"location":"SeasonUseEnum/#slots","title":"Slots","text":"Name Description season_use The seasons the space is occupied"},{"location":"SeasonUseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeasonUseEnum/#schema-source","title":"Schema Source","text":"name: season_use_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Spring:\n text: Spring\n Summer:\n text: Summer\n Fall:\n text: Fall\n Winter:\n text: Winter\n\nURI: SedimentTypeEnum
"},{"location":"SedimentTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description biogenous None cosmogenous None hydrogenous None lithogenous None"},{"location":"SedimentTypeEnum/#slots","title":"Slots","text":"Name Description sediment_type Information about the sediment type based on major constituents"},{"location":"SedimentTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SedimentTypeEnum/#schema-source","title":"Schema Source","text":"name: sediment_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n biogenous:\n text: biogenous\n cosmogenous:\n text: cosmogenous\n hydrogenous:\n text: hydrogenous\n lithogenous:\n text: lithogenous\n\nThe tool/substance used to separate or filter a solution or mixture.
URI: SeparationMethodEnum
"},{"location":"SeparationMethodEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description ptfe_96_well_filter_plate None syringe None"},{"location":"SeparationMethodEnum/#slots","title":"Slots","text":"Name Description separation_method The method that was used to separate a substance from a solution or mixture"},{"location":"SeparationMethodEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SeparationMethodEnum/#schema-source","title":"Schema Source","text":"name: SeparationMethodEnum\ndescription: The tool/substance used to separate or filter a solution or mixture.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\npermissible_values:\n ptfe_96_well_filter_plate:\n text: ptfe_96_well_filter_plate\n syringe:\n text: syringe\n\nURI: ShadingDeviceCondEnum
"},{"location":"ShadingDeviceCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"ShadingDeviceCondEnum/#slots","title":"Slots","text":"Name Description shading_device_cond The physical condition of the shading device at the time of sampling"},{"location":"ShadingDeviceCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceCondEnum/#schema-source","title":"Schema Source","text":"name: shading_device_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: ShadingDeviceTypeEnum
"},{"location":"ShadingDeviceTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bahama shutters None exterior roll blind None gambrel awning None hood awning None porchroller awning None sarasota shutters None slatted aluminum None solid aluminum awning None sun screen None tree None trellis None venetian awning None"},{"location":"ShadingDeviceTypeEnum/#slots","title":"Slots","text":"Name Description shading_device_type The type of shading device"},{"location":"ShadingDeviceTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"ShadingDeviceTypeEnum/#schema-source","title":"Schema Source","text":"name: shading_device_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bahama shutters:\n text: bahama shutters\n exterior roll blind:\n text: exterior roll blind\n gambrel awning:\n text: gambrel awning\n hood awning:\n text: hood awning\n porchroller awning:\n text: porchroller awning\n sarasota shutters:\n text: sarasota shutters\n slatted aluminum:\n text: slatted aluminum\n solid aluminum awning:\n text: solid aluminum awning\n sun screen:\n text: sun screen\n tree:\n text: tree\n trellis:\n text: trellis\n venetian awning:\n text: venetian awning\n\nNote
This is an abstract class and should not be instantiated directly.
URI: nmdc:Site
classDiagram\n class Site\n click Site href \"../Site\"\n MaterialEntity <|-- Site\n click MaterialEntity href \"../MaterialEntity\"\n\n\n Site <|-- FieldResearchSite\n click FieldResearchSite href \"../FieldResearchSite\"\n\n\n\n Site : alternative_identifiers\n\n Site : description\n\n Site : id\n\n Site : name\n\n Site : type\n\n\n\nname: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nclass_uri: nmdc:Site\n\nname: Site\ntitle: Site\ncomments:\n- BCO sample collection site ?\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: MaterialEntity\nabstract: true\nattributes:\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Site\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Site\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Site\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Site\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Site\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Site\n\nURI: SoilHorizonEnum
"},{"location":"SoilHorizonEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description O horizon None A horizon None E horizon None B horizon None C horizon None R layer None Permafrost None M horizon None"},{"location":"SoilHorizonEnum/#slots","title":"Slots","text":"Name Description soil_horizon Specific layer in the land area which measures parallel to the soil surface a..."},{"location":"SoilHorizonEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SoilHorizonEnum/#schema-source","title":"Schema Source","text":"name: soil_horizon_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n O horizon:\n text: O horizon\n A horizon:\n text: A horizon\n E horizon:\n text: E horizon\n B horizon:\n text: B horizon\n C horizon:\n text: C horizon\n R layer:\n text: R layer\n Permafrost:\n text: Permafrost\n M horizon:\n text: M horizon\n\nA string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
URI: xsd:string
base: str
uri: xsd:string
repr: str
URI: SpecificEnum
"},{"location":"SpecificEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description operation None as built None construction None bid None design None photos None"},{"location":"SpecificEnum/#slots","title":"Slots","text":"Name Description specific The building specifications"},{"location":"SpecificEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SpecificEnum/#schema-source","title":"Schema Source","text":"name: specific_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n operation:\n text: operation\n as built:\n text: as built\n construction:\n text: construction\n bid:\n text: bid\n design:\n text: design\n photos:\n text: photos\n\nURI: SrDepEnvEnum
"},{"location":"SrDepEnvEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Lacustine None Fluvioldeltaic None Fluviomarine None Marine None other None"},{"location":"SrDepEnvEnum/#slots","title":"Slots","text":"Name Description sr_dep_env Source rock depositional environment (https://en"},{"location":"SrDepEnvEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrDepEnvEnum/#schema-source","title":"Schema Source","text":"name: sr_dep_env_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Lacustine:\n text: Lacustine\n Fluvioldeltaic:\n text: Fluvioldeltaic\n Fluviomarine:\n text: Fluviomarine\n Marine:\n text: Marine\n other:\n text: other\n\nURI: SrGeolAgeEnum
"},{"location":"SrGeolAgeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Archean None Cambrian None Carboniferous None Cenozoic None Cretaceous None Devonian None Jurassic None Mesozoic None Neogene None Ordovician None Paleogene None Paleozoic None Permian None Precambrian None Proterozoic None Silurian None Triassic None other None"},{"location":"SrGeolAgeEnum/#slots","title":"Slots","text":"Name Description sr_geol_age Geological age of source rock (Additional info: https://en"},{"location":"SrGeolAgeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrGeolAgeEnum/#schema-source","title":"Schema Source","text":"name: sr_geol_age_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Archean:\n text: Archean\n Cambrian:\n text: Cambrian\n Carboniferous:\n text: Carboniferous\n Cenozoic:\n text: Cenozoic\n Cretaceous:\n text: Cretaceous\n Devonian:\n text: Devonian\n Jurassic:\n text: Jurassic\n Mesozoic:\n text: Mesozoic\n Neogene:\n text: Neogene\n Ordovician:\n text: Ordovician\n Paleogene:\n text: Paleogene\n Paleozoic:\n text: Paleozoic\n Permian:\n text: Permian\n Precambrian:\n text: Precambrian\n Proterozoic:\n text: Proterozoic\n Silurian:\n text: Silurian\n Triassic:\n text: Triassic\n other:\n text: other\n\nURI: SrKerogTypeEnum
"},{"location":"SrKerogTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Type I None Type II None Type III None Type IV None other None"},{"location":"SrKerogTypeEnum/#slots","title":"Slots","text":"Name Description sr_kerog_type Origin of kerogen"},{"location":"SrKerogTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrKerogTypeEnum/#schema-source","title":"Schema Source","text":"name: sr_kerog_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Type I:\n text: Type I\n Type II:\n text: Type II\n Type III:\n text: Type III\n Type IV:\n text: Type IV\n other:\n text: other\n\nURI: SrLithologyEnum
"},{"location":"SrLithologyEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Clastic None Carbonate None Coal None Biosilicieous None other None"},{"location":"SrLithologyEnum/#slots","title":"Slots","text":"Name Description sr_lithology Lithology of source rock (https://en"},{"location":"SrLithologyEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SrLithologyEnum/#schema-source","title":"Schema Source","text":"name: sr_lithology_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Clastic:\n text: Clastic\n Carbonate:\n text: Carbonate\n Coal:\n text: Coal\n Biosilicieous:\n text: Biosilicieous\n other:\n text: other\n\nThe type of stationary phase used in a chromatography process.
URI: StationaryPhaseEnum
"},{"location":"StationaryPhaseEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description BEH-HILIC None C18 None C8 None C4 None C2 None C1 None C30 None C60 None CNT None CN None Diol None HILIC None NH2 None Phenyl None Polysiloxane None PS-DVB None SAX None SCX None Silica None WCX None WAX None ZIC-HILIC None ZIC-pHILIC None ZIC-cHILIC None"},{"location":"StationaryPhaseEnum/#slots","title":"Slots","text":"Name Description stationary_phase The material the stationary phase is comprised of used in chromatography"},{"location":"StationaryPhaseEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StationaryPhaseEnum/#schema-source","title":"Schema Source","text":"name: StationaryPhaseEnum\ndescription: The type of stationary phase used in a chromatography process.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-4504-1039\nrank: 1000\npermissible_values:\n BEH-HILIC:\n text: BEH-HILIC\n C18:\n text: C18\n C8:\n text: C8\n C4:\n text: C4\n C2:\n text: C2\n C1:\n text: C1\n C30:\n text: C30\n C60:\n text: C60\n CNT:\n text: CNT\n CN:\n text: CN\n Diol:\n text: Diol\n HILIC:\n text: HILIC\n NH2:\n text: NH2\n Phenyl:\n text: Phenyl\n Polysiloxane:\n text: Polysiloxane\n PS-DVB:\n text: PS-DVB\n SAX:\n text: SAX\n SCX:\n text: SCX\n Silica:\n text: Silica\n WCX:\n text: WCX\n WAX:\n text: WAX\n ZIC-HILIC:\n text: ZIC-HILIC\n ZIC-pHILIC:\n text: ZIC-pHILIC\n ZIC-cHILIC:\n text: ZIC-cHILIC\n\nURI: StatusEnum
"},{"location":"StatusEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description pass None fail None"},{"location":"StatusEnum/#slots","title":"Slots","text":"Name Description qc_status Stores information about the result of a process (ie the process of sequencin..."},{"location":"StatusEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StatusEnum/#schema-source","title":"Schema Source","text":"name: StatusEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n pass:\n text: pass\n fail:\n text: fail\n\nA planned process with the objective to preserve and protect material entities by placing them in an identified location which may have a controlled environment.
URI: nmdc:StorageProcess
classDiagram\n class StorageProcess\n click StorageProcess href \"../StorageProcess\"\n PlannedProcess <|-- StorageProcess\n click PlannedProcess href \"../PlannedProcess\"\n\n\n\n StorageProcess : alternative_identifiers\n\n StorageProcess : contained_in\n\n StorageProcess --> \"0..1\" ContainerCategoryEnum : contained_in\n click ContainerCategoryEnum href \"../ContainerCategoryEnum\"\n\n StorageProcess : description\n\n StorageProcess : end_date\n\n StorageProcess : has_failure_categorization\n\n StorageProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n StorageProcess : has_input\n\n StorageProcess --> \"*\" NamedThing : has_input\n click NamedThing href \"../NamedThing\"\n\n StorageProcess : has_output\n\n StorageProcess --> \"*\" NamedThing : has_output\n click NamedThing href \"../NamedThing\"\n\n StorageProcess : id\n\n StorageProcess : name\n\n StorageProcess : processing_institution\n\n StorageProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n StorageProcess : protocol_link\n\n StorageProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n StorageProcess : qc_comment\n\n StorageProcess : qc_status\n\n StorageProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n StorageProcess : start_date\n\n StorageProcess : substances_used\n\n StorageProcess --> \"*\" PortionOfSubstance : substances_used\n click PortionOfSubstance href \"../PortionOfSubstance\"\n\n StorageProcess : temperature\n\n StorageProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n StorageProcess : type\n\n\n\nname: StorageProcess\ndescription: A planned process with the objective to preserve and protect material\n entities by placing them in an identified location which may have a controlled\n environment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0302893\nis_a: PlannedProcess\nslots:\n- substances_used\n- contained_in\n- temperature\nslot_usage:\n substances_used:\n name: substances_used\n description: The substance(s) that a processed sample is stored in.\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:StorageProcess\n\nname: StorageProcess\ndescription: A planned process with the objective to preserve and protect material\n entities by placing them in an identified location which may have a controlled\n environment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0302893\nis_a: PlannedProcess\nslot_usage:\n substances_used:\n name: substances_used\n description: The substance(s) that a processed sample is stored in.\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_input:\n name: has_input\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n substances_used:\n name: substances_used\n description: The substance(s) that a processed sample is stored in.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: substances_used\n owner: StorageProcess\n domain_of:\n - Extraction\n - StorageProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n - MobilePhaseSegment\n range: PortionOfSubstance\n multivalued: true\n inlined: true\n inlined_as_list: true\n contained_in:\n name: contained_in\n description: A type of container.\n examples:\n - value: test tube\n - value: falcon tube\n - value: whirlpak\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contained_in\n owner: StorageProcess\n domain_of:\n - SubSamplingProcess\n - StorageProcess\n range: ContainerCategoryEnum\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: StorageProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: StorageProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: StorageProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:storpr-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: StorageProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: StorageProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: StorageProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: StorageProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:StorageProcess\n\nThis enumeration specifies information about stranded RNA library preparations.
URI: StrandedOrientationEnum
"},{"location":"StrandedOrientationEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description antisense orientation None Orientation that is complementary (non-coding) to a sequence of messenger RNA sense orientation None Orientation that corresponds to the coding sequence of messenger RNA"},{"location":"StrandedOrientationEnum/#slots","title":"Slots","text":"Name Description stranded_orientation Lists the strand orientiation for a stranded RNA library preparation"},{"location":"StrandedOrientationEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StrandedOrientationEnum/#schema-source","title":"Schema Source","text":"name: StrandedOrientationEnum\ndescription: This enumeration specifies information about stranded RNA library preparations.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n antisense orientation:\n text: antisense orientation\n description: Orientation that is complementary (non-coding) to a sequence of messenger\n RNA.\n comments:\n - See https://www.genome.gov/genetics-glossary/antisense\n exact_mappings:\n - SO:0000077\n sense orientation:\n text: sense orientation\n description: Orientation that corresponds to the coding sequence of messenger\n RNA.\n\nA character string
URI: xsd:string
base: str
uri: xsd:string
A study summarizes the overall goal of a research initiative and outlines the key objective of its underlying projects.
URI: nmdc:Study
classDiagram\n class Study\n click Study href \"../Study\"\n NamedThing <|-- Study\n click NamedThing href \"../NamedThing\"\n\n\n\n Study : alternative_descriptions\n\n Study : alternative_identifiers\n\n Study : alternative_names\n\n Study : alternative_titles\n\n Study : associated_dois\n\n Study --> \"*\" Doi : associated_dois\n click Doi href \"../Doi\"\n\n Study : description\n\n Study : ecosystem\n\n Study : ecosystem_category\n\n Study : ecosystem_subtype\n\n Study : ecosystem_type\n\n Study : emsl_project_identifiers\n\n Study : funding_sources\n\n Study : gnps_task_identifiers\n\n Study : gold_study_identifiers\n\n Study : has_credit_associations\n\n Study --> \"*\" CreditAssociation : has_credit_associations\n click CreditAssociation href \"../CreditAssociation\"\n\n Study : homepage_website\n\n Study : id\n\n Study : insdc_bioproject_identifiers\n\n Study : jgi_portal_study_identifiers\n\n Study : mgnify_project_identifiers\n\n Study : name\n\n Study : neon_study_identifiers\n\n Study : notes\n\n Study : objective\n\n Study : part_of\n\n Study --> \"*\" Study : part_of\n click Study href \"../Study\"\n\n Study : principal_investigator\n\n Study --> \"0..1\" PersonValue : principal_investigator\n click PersonValue href \"../PersonValue\"\n\n Study : protocol_link\n\n Study --> \"*\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n Study : related_identifiers\n\n Study : specific_ecosystem\n\n Study : study_category\n\n Study --> \"1\" StudyCategoryEnum : study_category\n click StudyCategoryEnum href \"../StudyCategoryEnum\"\n\n Study : study_image\n\n Study --> \"*\" ImageValue : study_image\n click ImageValue href \"../ImageValue\"\n\n Study : title\n\n Study : type\n\n Study : websites\n\n\n\nname: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n the key objective of its underlying projects.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A study (project) groups together data submitted to the archive and\n controls its release date. A study accession is typically used when citing data\n submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research initiative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslots:\n- emsl_project_identifiers\n- gnps_task_identifiers\n- gold_study_identifiers\n- insdc_bioproject_identifiers\n- jgi_portal_study_identifiers\n- mgnify_project_identifiers\n- neon_study_identifiers\n- related_identifiers\n- alternative_descriptions\n- alternative_names\n- alternative_titles\n- ecosystem\n- ecosystem_category\n- ecosystem_subtype\n- ecosystem_type\n- specific_ecosystem\n- associated_dois\n- funding_sources\n- has_credit_associations\n- homepage_website\n- notes\n- objective\n- part_of\n- principal_investigator\n- protocol_link\n- study_category\n- study_image\n- title\n- websites\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a name for the study your samples will belong with.\n websites:\n name: websites\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n homepage_website:\n name: homepage_website\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the consortium's homepage if the study_category is a consortium.\n description:\n name: description\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n notes:\n name: notes\n annotations:\n tooltip:\n tag: tooltip\n value: Add any additional notes or comments about this study.\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n alternative_names:\n name: alternative_names\n annotations:\n tooltip:\n tag: tooltip\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n part_of:\n name: part_of\n description: Links a study or consortium to a parent (or umbrella) study or consortium.\n comments:\n - Value is the id of the umbrella study or consortium.\n range: Study\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n protocol_link:\n name: protocol_link\n multivalued: true\n inlined_as_list: true\nclass_uri: nmdc:Study\n\nname: Study\ndescription: A study summarizes the overall goal of a research initiative and outlines\n the key objective of its underlying projects.\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: A study (project) groups together data submitted to the archive and\n controls its release date. A study accession is typically used when citing data\n submitted to ENA\ntodos:\n- determine how to get data values for submitted_to_insdc, investigation_type, experimental_factor\n- project_name is redundant with name, so excluding it\nnotes:\n- sample GOLD link https://bioregistry.io/gold:Gs0110115\n- sample insdc.srs link https://www.ebi.ac.uk/ena/browser/view/PRJEB45055 ?\n- sample mgnify link https://www.ebi.ac.uk/metagenomics/studies/MGYS00005757\n- GOLD, insdc.srs and mgnify are reasonable prefixes for alternative study identifiers,\n but no longer for the Study.id\ncomments:\n- The Study class can include both consortia and research studies.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- proposal\n- research proposal\n- research study\n- investigation\n- project\n- umbrella project\n- research initiative\nexact_mappings:\n- OBI:0000066\n- SIO:000747\n- NCIT:C41198\n- ISA:Investigation\nbroad_mappings:\n- prov:Activity\nis_a: NamedThing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a name for the study your samples will belong with.\n websites:\n name: websites\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n homepage_website:\n name: homepage_website\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the consortium's homepage if the study_category is a consortium.\n description:\n name: description\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n notes:\n name: notes\n annotations:\n tooltip:\n tag: tooltip\n value: Add any additional notes or comments about this study.\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n alternative_names:\n name: alternative_names\n annotations:\n tooltip:\n tag: tooltip\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n part_of:\n name: part_of\n description: Links a study or consortium to a parent (or umbrella) study or consortium.\n comments:\n - Value is the id of the umbrella study or consortium.\n range: Study\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n protocol_link:\n name: protocol_link\n multivalued: true\n inlined_as_list: true\nattributes:\n emsl_project_identifiers:\n name: emsl_project_identifiers\n description: Identifiers that link a NMDC study to the EMSL user facility website\n hosting the project description of an EMSL user project\n title: EMSL Project Identifiers\n todos:\n - elaborate on description\n notes:\n - these identifiers are all currently 5 digits long but that could change in the\n future\n examples:\n - value: emsl.project:60141\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/927#issuecomment-1802136437\n rank: 1000\n is_a: study_identifiers\n mixins:\n - emsl_identifiers\n alias: emsl_project_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^emsl\\.project:[0-9]{5}$\n gnps_task_identifiers:\n name: gnps_task_identifiers\n description: identifiers that link a NMDC study to a web-based report about metabolomics\n analysis progress and results\n title: GNPS task identifiers\n comments:\n - this could be considered a related identifier, as the metabolomics progress\n and results aren't a study per se\n - this identifier was registered with bioregistry but not identifiers.org\n examples:\n - value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysis/\n rank: 1000\n is_a: study_identifiers\n mixins:\n - gnps_identifiers\n alias: gnps_task_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^gnps\\.task:[a-f0-9]+$\n gold_study_identifiers:\n name: gold_study_identifiers\n description: identifiers for corresponding project(s) in GOLD\n title: GOLD Study Identifiers\n comments:\n - uses the prefix GS (but possibly in a different case)\n examples:\n - value: https://bioregistry.io/gold:Gs0110115\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/studies\n rank: 1000\n is_a: study_identifiers\n mixins:\n - gold_identifiers\n alias: gold_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^gold:Gs[0-9]+$\n insdc_bioproject_identifiers:\n name: insdc_bioproject_identifiers\n annotations:\n tooltip:\n tag: tooltip\n value: Provide the NCBI BioProject Accession Number associated with the listed\n NCBI BioProject Title.\n description: Unique identifier for a bioproject submitted to INSDC that relates\n to the NMDC submitted study.\n comments:\n - these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n one to one\n examples:\n - value: https://bioregistry.io/bioproject:PRJNA366857\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2\n metatranscriptome\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://www.ncbi.nlm.nih.gov/bioproject/\n - https://www.ddbj.nig.ac.jp/bioproject/index-e.html\n aliases:\n - NCBI bioproject identifiers\n - DDBJ bioproject identifiers\n rank: 1000\n is_a: study_identifiers\n mixins:\n - insdc_identifiers\n alias: insdc_bioproject_identifiers\n owner: Study\n domain_of:\n - NucleotideSequencing\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n jgi_portal_study_identifiers:\n name: jgi_portal_study_identifiers\n id_prefixes:\n - jgi.proposal\n description: Identifiers that link a NMDC study to a website hosting raw and analyzed\n data for a JGI proposal. The suffix of the curie can used to query the GOLD\n API and is interoperable with an award DOI from OSTI and a GOLD study identifier.\n title: JGI Portal Study identifiers\n comments:\n - Could this could be considered a related identifier?\n - Curie suffix is the Site Award Number from an OSTI award page\n - Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD\n study identifier gold:Gs0154044\n - bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\n examples:\n - value: jgi.proposal:507130\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - jgi_portal_identifiers\n alias: jgi_portal_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^jgi.proposal:\\d+$\n mgnify_project_identifiers:\n name: mgnify_project_identifiers\n description: identifiers for corresponding project in MGnify\n examples:\n - value: https://bioregistry.io/mgnify.proj:MGYS00005757\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - mgnify_identifiers\n alias: mgnify_project_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^mgnify.proj:[A-Z]+[0-9]+$\n neon_study_identifiers:\n name: neon_study_identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: study_identifiers\n mixins:\n - neon_identifiers\n alias: neon_study_identifiers\n owner: Study\n domain_of:\n - Study\n range: external_identifier\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n related_identifiers:\n name: related_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Similar, but not necessarily identical to that which has been submitted to NMDC\n title: Related Identifiers\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: related_identifiers\n owner: Study\n domain_of:\n - Study\n range: string\n alternative_descriptions:\n name: alternative_descriptions\n description: A list of alternative descriptions for the entity. The distinction\n between description and alternative descriptions is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_descriptions\n owner: Study\n domain_of:\n - Study\n range: string\n multivalued: true\n alternative_names:\n name: alternative_names\n annotations:\n tooltip:\n tag: tooltip\n value: Project, study, or sample set names the are also associated with this\n submission or other names / identifiers for this study.\n description: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n - skos:altLabel\n rank: 1000\n alias: alternative_names\n owner: Study\n domain_of:\n - OntologyClass\n - Study\n range: string\n multivalued: true\n alternative_titles:\n name: alternative_titles\n description: A list of alternative titles for the entity. The distinction between\n title and alternative titles is application-specific.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:alternative\n rank: 1000\n alias: alternative_titles\n owner: Study\n domain_of:\n - Study\n range: string\n multivalued: true\n ecosystem:\n name: ecosystem\n description: An ecosystem is a combination of a physical environment (abiotic\n factors) and all the organisms (biotic factors) that interact with this environment.\n Ecosystem is in position 1/5 in a GOLD path.\n comments:\n - The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism\n or environmental sample is collected. The three broad groups under Ecosystem\n are Environmental, Host-associated, and Engineered. They represent samples collected\n from a natural environment or from another organism or from engineered environments\n like bioreactors respectively.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_category:\n name: ecosystem_category\n description: Ecosystem categories represent divisions within the ecosystem based\n on specific characteristics of the environment from where an organism or sample\n is isolated. Ecosystem category is in position 2/5 in a GOLD path.\n comments:\n - The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or\n phyla and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_category\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_subtype:\n name: ecosystem_subtype\n description: Ecosystem subtypes represent further subdivision of Ecosystem types\n into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD\n path.\n comments:\n - Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided\n (for example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in\n the Ecosystem subtype category.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_subtype\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n ecosystem_type:\n name: ecosystem_type\n description: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still\n broad but specific to the characteristics of a given environment. Ecosystem\n type is in position 3/5 in a GOLD path.\n comments:\n - The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor\n air as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: ecosystem_type\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n specific_ecosystem:\n name: specific_ecosystem\n description: Specific ecosystems represent specific features of the environment\n like aphotic zone in an ocean or gastric mucosa within a host digestive system.\n Specific ecosystem is in position 5/5 in a GOLD path.\n comments:\n - Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://gold.jgi.doe.gov/help\n rank: 1000\n is_a: gold_path_field\n alias: specific_ecosystem\n owner: Study\n domain_of:\n - Biosample\n - Study\n range: string\n associated_dois:\n name: associated_dois\n description: A list of DOIs associated with a resource, such as a list of DOIS\n associated with a Study.\n examples:\n - value: '[{''doi'': ''doi:10.46936/intm.proj.2021.60141/60000423'', ''doi_provider'':\n ''emsl'', ''doi_category'': ''award_doi''}, {''doi'': ''doi:10.1101/2022.12.12.520098'',\n ''doi_category'': ''publication_doi''}, {''doi'': ''doi:10.48321/D1Z60Q'',\n ''doi_category'': ''data_management_plan_doi'', ''doi_provider'': ''gsc''}]'\n description: Provides a list of two DOIs; specifically, an EMSL award DOI and\n a publication DOI.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - Associated DOIs\n - Associated digital object identifiers\n rank: 1000\n alias: associated_dois\n owner: Study\n domain_of:\n - Study\n range: Doi\n multivalued: true\n inlined: true\n inlined_as_list: true\n funding_sources:\n name: funding_sources\n description: A list of organizations, along with the award numbers, that underwrite\n financial support for projects of a particular type. Typically, they process\n applications and award funds to the chosen qualified applicants.\n comments:\n - Include only the name of the funding organization and the award or contract\n number.\n examples:\n - value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n - value: U.S. Department of Energy, Office of Science, Office of Biological and\n Environmental Research (BER) under contract DE-AC05-00OR2275\n from_schema: https://w3id.org/nmdc/nmdc\n close_mappings:\n - NCIT:C39409\n rank: 1000\n alias: funding_sources\n owner: Study\n domain_of:\n - Study\n range: string\n multivalued: true\n has_credit_associations:\n name: has_credit_associations\n annotations:\n tooltip:\n tag: tooltip\n value: Other researchers associated with this study.\n description: 'This slot links a study to a credit association. The credit association\n will be linked to a person value and to a CRediT Contributor Roles term. Overall\n semantics: person should get credit X for their participation in the study'\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: prov:qualifiedAssociation\n alias: has_credit_associations\n owner: Study\n domain_of:\n - Study\n range: CreditAssociation\n multivalued: true\n inlined: true\n inlined_as_list: true\n homepage_website:\n name: homepage_website\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the consortium's homepage if the study_category is a consortium.\n description: The website address (URL) of an entity's homepage.\n examples:\n - value: https://www.neonscience.org/\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n is_a: websites\n alias: homepage_website\n owner: Study\n domain_of:\n - Study\n range: string\n multivalued: true\n pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n maximum_cardinality: 1\n notes:\n name: notes\n annotations:\n tooltip:\n tag: tooltip\n value: Add any additional notes or comments about this study.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: notes\n owner: Study\n domain_of:\n - Study\n range: string\n objective:\n name: objective\n description: The scientific objectives associated with the entity. It SHOULD correspond\n to scientific norms for objectives field in a structured abstract.\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - SIO:000337\n rank: 1000\n alias: objective\n owner: Study\n domain_of:\n - Study\n range: string\n part_of:\n name: part_of\n description: Links a study or consortium to a parent (or umbrella) study or consortium.\n comments:\n - Value is the id of the umbrella study or consortium.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - is part of\n rank: 1000\n slot_uri: dcterms:isPartOf\n alias: part_of\n owner: Study\n domain_of:\n - FieldResearchSite\n - Study\n range: Study\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n principal_investigator:\n name: principal_investigator\n description: Principal Investigator who led the study and/or generated the dataset.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - PI\n rank: 1000\n alias: principal_investigator\n owner: Study\n domain_of:\n - Study\n - DataGeneration\n range: PersonValue\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: Study\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n multivalued: true\n inlined_as_list: true\n study_category:\n name: study_category\n description: The type of research initiative\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: study_category\n owner: Study\n domain_of:\n - Study\n range: StudyCategoryEnum\n required: true\n study_image:\n name: study_image\n description: Links a study to one or more images.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: study_image\n owner: Study\n domain_of:\n - Study\n range: ImageValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n title:\n name: title\n description: A name given to the entity that differs from the name/label programmatically\n assigned to it. For example, when extracting study information for GOLD, the\n GOLD system has assigned a name/label. However, for display purposes, we may\n also wish the capture the title of the proposal that was used to fund the study.\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - dcterms:title\n rank: 1000\n alias: title\n owner: Study\n domain_of:\n - Study\n range: string\n websites:\n name: websites\n annotations:\n tooltip:\n tag: tooltip\n value: Link to the Principal Investigator's research lab webpage or the study\n webpage associated with this collection of samples. Multiple links can be\n provided.\n description: A list of websites that are associated with the entity.\n comments:\n - DOIs should not be included as websites. Instead, use the associated_dois slot.\n - A consortium's homepage website should be included in the homepage_website slot,\n not in websites.\n - consortium is a convenience term for a Study whose study_category value is consortium\n - the website slot and its subproperties are virtually identical to the url slot,\n except that they are multivalued and url is single-valued.\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - nmdc:url\n rank: 1000\n alias: websites\n owner: Study\n domain_of:\n - PersonValue\n - Study\n range: string\n multivalued: true\n pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: Study\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a name for the study your samples will belong with.\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: Study\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n annotations:\n tooltip:\n tag: tooltip\n value: Provide a brief description of your study.\n description: A brief, link-free summary of a Study\n comments:\n - Include links in other Study slots, such as websites or dois.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: Study\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: Unique identifier for a study submitted to additional resources.\n Matches that which has been submitted to NMDC\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: Study\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: Study\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:Study\n\nURI: StudyCategoryEnum
"},{"location":"StudyCategoryEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description research_study None A detailed examination, analysis, or critical inspection of a hypothesis-driv... consortium None A group formed to undertake a venture that is beyond the capabilities of the ..."},{"location":"StudyCategoryEnum/#slots","title":"Slots","text":"Name Description study_category The type of research initiative"},{"location":"StudyCategoryEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"StudyCategoryEnum/#schema-source","title":"Schema Source","text":"name: StudyCategoryEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n research_study:\n text: research_study\n description: A detailed examination, analysis, or critical inspection of a hypothesis-driven\n experiment.\n exact_mappings:\n - SIO:001066\n - NCIT:C63536\n - ISA:Study\n close_mappings:\n - OBI:0000355\n consortium:\n text: consortium\n description: A group formed to undertake a venture that is beyond the capabilities\n of the individual members. Each member of the consortium brings a high level\n of expertise in a specific area to ensure the successful completion of the project.\n comments:\n - A consortium has collections of data, those data do not come from a hypothesis-driven\n experiment.\n exact_mappings:\n - NCIT:C61538\n\nSeparating a sample aliquot from the starting material for downstream activity.
__
URI: nmdc:SubSamplingProcess
classDiagram\n class SubSamplingProcess\n click SubSamplingProcess href \"../SubSamplingProcess\"\n MaterialProcessing <|-- SubSamplingProcess\n click MaterialProcessing href \"../MaterialProcessing\"\n\n\n\n SubSamplingProcess : alternative_identifiers\n\n SubSamplingProcess : contained_in\n\n SubSamplingProcess --> \"0..1\" ContainerCategoryEnum : contained_in\n click ContainerCategoryEnum href \"../ContainerCategoryEnum\"\n\n SubSamplingProcess : container_size\n\n SubSamplingProcess --> \"0..1\" QuantityValue : container_size\n click QuantityValue href \"../QuantityValue\"\n\n SubSamplingProcess : description\n\n SubSamplingProcess : end_date\n\n SubSamplingProcess : has_failure_categorization\n\n SubSamplingProcess --> \"*\" FailureCategorization : has_failure_categorization\n click FailureCategorization href \"../FailureCategorization\"\n\n SubSamplingProcess : has_input\n\n SubSamplingProcess --> \"*\" Sample : has_input\n click Sample href \"../Sample\"\n\n SubSamplingProcess : has_output\n\n SubSamplingProcess --> \"*\" ProcessedSample : has_output\n click ProcessedSample href \"../ProcessedSample\"\n\n SubSamplingProcess : id\n\n SubSamplingProcess : instrument_used\n\n SubSamplingProcess --> \"*\" Instrument : instrument_used\n click Instrument href \"../Instrument\"\n\n SubSamplingProcess : mass\n\n SubSamplingProcess --> \"0..1\" QuantityValue : mass\n click QuantityValue href \"../QuantityValue\"\n\n SubSamplingProcess : name\n\n SubSamplingProcess : processing_institution\n\n SubSamplingProcess --> \"0..1\" ProcessingInstitutionEnum : processing_institution\n click ProcessingInstitutionEnum href \"../ProcessingInstitutionEnum\"\n\n SubSamplingProcess : protocol_link\n\n SubSamplingProcess --> \"0..1\" Protocol : protocol_link\n click Protocol href \"../Protocol\"\n\n SubSamplingProcess : qc_comment\n\n SubSamplingProcess : qc_status\n\n SubSamplingProcess --> \"0..1\" StatusEnum : qc_status\n click StatusEnum href \"../StatusEnum\"\n\n SubSamplingProcess : sampled_portion\n\n SubSamplingProcess --> \"*\" SamplePortionEnum : sampled_portion\n click SamplePortionEnum href \"../SamplePortionEnum\"\n\n SubSamplingProcess : start_date\n\n SubSamplingProcess : temperature\n\n SubSamplingProcess --> \"0..1\" QuantityValue : temperature\n click QuantityValue href \"../QuantityValue\"\n\n SubSamplingProcess : type\n\n SubSamplingProcess : volume\n\n SubSamplingProcess --> \"0..1\" QuantityValue : volume\n click QuantityValue href \"../QuantityValue\"\n\n\n\nname: SubSamplingProcess\ndescription: 'Separating a sample aliquot from the starting material for downstream\n activity.\n\n '\nnotes:\n- A subsample may be (a) a portion of the sample obtained by selection or division;\n (b) an individual unit of the lot taken as part of the sample; (c) the final unit\n of multistage sampling. The term 'subsample' is used either in the sense of a 'sample\n of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent\n from the context or is defined.\n- TODO - Montana to visit slot descriptions\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0000744\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslots:\n- container_size\n- contained_in\n- temperature\n- volume\n- mass\n- sampled_portion\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The output volume of the SubSampling Process.\n mass:\n name: mass\n description: The output mass of the SubSampling Process.\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The subsample.\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\nclass_uri: nmdc:SubSamplingProcess\n\nname: SubSamplingProcess\ndescription: 'Separating a sample aliquot from the starting material for downstream\n activity.\n\n '\nnotes:\n- A subsample may be (a) a portion of the sample obtained by selection or division;\n (b) an individual unit of the lot taken as part of the sample; (c) the final unit\n of multistage sampling. The term 'subsample' is used either in the sense of a 'sample\n of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent\n from the context or is defined.\n- TODO - Montana to visit slot descriptions\nfrom_schema: https://w3id.org/nmdc/nmdc\nrelated_mappings:\n- OBI:0000744\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\n- ORCID:0000-0001-9076-6066\n- ORCID:0009-0008-4013-7737\nis_a: MaterialProcessing\nslot_usage:\n id:\n name: id\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n interpolated: true\n volume:\n name: volume\n description: The output volume of the SubSampling Process.\n mass:\n name: mass\n description: The output mass of the SubSampling Process.\n has_input:\n name: has_input\n range: Sample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The subsample.\n range: ProcessedSample\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\nattributes:\n container_size:\n name: container_size\n description: The volume of the container an analyte is stored in or an activity\n takes place in\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: container_size\n owner: SubSamplingProcess\n domain_of:\n - SubSamplingProcess\n - FiltrationProcess\n range: QuantityValue\n contained_in:\n name: contained_in\n description: A type of container.\n examples:\n - value: test tube\n - value: falcon tube\n - value: whirlpak\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: contained_in\n owner: SubSamplingProcess\n domain_of:\n - SubSamplingProcess\n - StorageProcess\n range: ContainerCategoryEnum\n temperature:\n name: temperature\n description: The value of a temperature measurement or temperature used in a process.\n notes:\n - Not to be confused with the MIXS:0000113\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: temperature\n owner: SubSamplingProcess\n domain_of:\n - ChromatographyConfiguration\n - SubSamplingProcess\n - StorageProcess\n - ChromatographicSeparationProcess\n - DissolvingProcess\n - ChemicalConversionProcess\n range: QuantityValue\n volume:\n name: volume\n description: The output volume of the SubSampling Process.\n from_schema: https://w3id.org/nmdc/nmdc\n contributors:\n - ORCID:0009-0001-1555-1601\n - ORCID:0000-0002-8683-0050\n rank: 1000\n alias: volume\n owner: SubSamplingProcess\n domain_of:\n - Extraction\n - SubSamplingProcess\n - FiltrationProcess\n - MobilePhaseSegment\n - PortionOfSubstance\n range: QuantityValue\n mass:\n name: mass\n description: The output mass of the SubSampling Process.\n title: mass\n from_schema: https://w3id.org/nmdc/nmdc\n exact_mappings:\n - PATO:0000125\n rank: 1000\n alias: mass\n owner: SubSamplingProcess\n domain_of:\n - SubSamplingProcess\n - PortionOfSubstance\n range: QuantityValue\n sampled_portion:\n name: sampled_portion\n description: The portion of the sample that is taken for downstream activity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: sampled_portion\n owner: SubSamplingProcess\n domain_of:\n - SubSamplingProcess\n range: SamplePortionEnum\n multivalued: true\n instrument_used:\n name: instrument_used\n description: What instrument was used during DataGeneration or MaterialProcessing.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: instrument_used\n owner: SubSamplingProcess\n domain_of:\n - MaterialProcessing\n - DataGeneration\n range: Instrument\n multivalued: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: Sample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: The subsample.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: ProcessedSample\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: SubSamplingProcess\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: SubSamplingProcess\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'\n interpolated: true\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: SubSamplingProcess\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: SubSamplingProcess\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: SubSamplingProcess\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: SubSamplingProcess\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:SubSamplingProcess\n\nURI: SubstanceRoleEnum
"},{"location":"SubstanceRoleEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description buffer CHEBI:35225 Maintains the pH of the solution within a specific range to stabilize analyte... acid CHEBI:37527 Donates a proton or accepts an electron pair in a chemical reaction base CHEBI:22695 Accepts a proton or donates an electron pair in a chemical reaction ms_proteolytic_enzyme MS:1002986 Enzyme that catalyzes the hydrolysis of proteins and is used in mass spectrom... solvent CHEBI:46787 Dissolves the sample or reagents to facilitate reactions or extraction surfactant CHEBI:35195 Reduces surface tension and aids in the solubilization of substances derivatizing_agent None Chemically modifies analytes to improve detection or separation solubilizing_agent None"},{"location":"SubstanceRoleEnum/#slots","title":"Slots","text":"Name Description substance_role The role of a substance in a process"},{"location":"SubstanceRoleEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstanceRoleEnum/#schema-source","title":"Schema Source","text":"name: SubstanceRoleEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n buffer:\n text: buffer\n description: Maintains the pH of the solution within a specific range to stabilize\n analytes or reactions.\n meaning: CHEBI:35225\n acid:\n text: acid\n description: Donates a proton or accepts an electron pair in a chemical reaction.\n meaning: CHEBI:37527\n base:\n text: base\n description: Accepts a proton or donates an electron pair in a chemical reaction.\n meaning: CHEBI:22695\n ms_proteolytic_enzyme:\n text: ms_proteolytic_enzyme\n description: Enzyme that catalyzes the hydrolysis of proteins and is used in mass\n spectrometry based proteomics\n meaning: MS:1002986\n solvent:\n text: solvent\n description: Dissolves the sample or reagents to facilitate reactions or extraction.\n meaning: CHEBI:46787\n surfactant:\n text: surfactant\n description: Reduces surface tension and aids in the solubilization of substances.\n meaning: CHEBI:35195\n derivatizing_agent:\n text: derivatizing_agent\n description: Chemically modifies analytes to improve detection or separation.\n solubilizing_agent:\n text: solubilizing_agent\n\nURI: SubstructureTypeEnum
"},{"location":"SubstructureTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crawlspace None slab on grade None basement None"},{"location":"SubstructureTypeEnum/#slots","title":"Slots","text":"Name Description substructure_type The substructure or under building is that largely hidden section of the buil..."},{"location":"SubstructureTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SubstructureTypeEnum/#schema-source","title":"Schema Source","text":"name: substructure_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crawlspace:\n text: crawlspace\n slab on grade:\n text: slab on grade\n basement:\n text: basement\n\nURI: SurfAirContEnum
"},{"location":"SurfAirContEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description dust None organic matter None particulate matter None volatile organic compounds None biological contaminants None radon None nutrients None biocides None"},{"location":"SurfAirContEnum/#slots","title":"Slots","text":"Name Description surf_air_cont Contaminant identified on surface"},{"location":"SurfAirContEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfAirContEnum/#schema-source","title":"Schema Source","text":"name: surf_air_cont_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n dust:\n text: dust\n organic matter:\n text: organic matter\n particulate matter:\n text: particulate matter\n volatile organic compounds:\n text: volatile organic compounds\n biological contaminants:\n text: biological contaminants\n radon:\n text: radon\n nutrients:\n text: nutrients\n biocides:\n text: biocides\n\nURI: SurfMaterialEnum
"},{"location":"SurfMaterialEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description adobe None carpet None cinder blocks None concrete None hay bales None glass None metal None paint None plastic None stainless steel None stone None stucco None tile None vinyl None wood None"},{"location":"SurfMaterialEnum/#slots","title":"Slots","text":"Name Description surf_material Surface materials at the point of sampling"},{"location":"SurfMaterialEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"SurfMaterialEnum/#schema-source","title":"Schema Source","text":"name: surf_material_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n adobe:\n text: adobe\n carpet:\n text: carpet\n cinder blocks:\n text: cinder blocks\n concrete:\n text: concrete\n hay bales:\n text: hay bales\n glass:\n text: glass\n metal:\n text: metal\n paint:\n text: paint\n plastic:\n text: plastic\n stainless steel:\n text: stainless steel\n stone:\n text: stone\n stucco:\n text: stucco\n tile:\n text: tile\n vinyl:\n text: vinyl\n wood:\n text: wood\n\nURI: TargetGeneEnum
"},{"location":"TargetGeneEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description 16S_rRNA None the small subunit of the bacterial/archean ribosome 23S_rRNA None the large subunit of the bacterial/archean ribosome 18S_rRNA None the small subunit of the eukaryotic ribosome 28S_rRNA None the large subunit of the eukaryotic ribosome"},{"location":"TargetGeneEnum/#slots","title":"Slots","text":"Name Description target_gene Targeted gene or locus name for marker gene studies"},{"location":"TargetGeneEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TargetGeneEnum/#schema-source","title":"Schema Source","text":"name: TargetGeneEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 16S_rRNA:\n text: 16S_rRNA\n description: the small subunit of the bacterial/archean ribosome\n aliases:\n - 16S rRNA\n - 16S ribosomal RNA\n narrow_mappings:\n - OBI:0002763\n 23S_rRNA:\n text: 23S_rRNA\n description: the large subunit of the bacterial/archean ribosome\n aliases:\n - 23S rRNA\n - 23S ribosomal RNA\n 18S_rRNA:\n text: 18S_rRNA\n description: the small subunit of the eukaryotic ribosome\n aliases:\n - 18S rRNA\n - 18S ribosomal RNA\n 28S_rRNA:\n text: 28S_rRNA\n description: the large subunit of the eukaryotic ribosome\n aliases:\n - -28S rRNA - 28S ribosomal RNA\n\nA basic string value
URI: nmdc:TextValue
classDiagram\n class TextValue\n click TextValue href \"../TextValue\"\n AttributeValue <|-- TextValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n TextValue : has_raw_value\n\n TextValue : language\n\n TextValue : type\n\n\n\nname: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nslots:\n- language\nclass_uri: nmdc:TextValue\n\nname: TextValue\ndescription: A basic string value\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n language:\n name: language\n description: Should use ISO 639-1 code e.g. \"en\", \"fr\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: language\n owner: TextValue\n domain_of:\n - TextValue\n range: language_code\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: TextValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: TextValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:TextValue\n\nURI: TidalStageEnum
"},{"location":"TidalStageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description low tide None ebb tide None flood tide None high tide None"},{"location":"TidalStageEnum/#slots","title":"Slots","text":"Name Description tidal_stage Stage of tide"},{"location":"TidalStageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TidalStageEnum/#schema-source","title":"Schema Source","text":"name: tidal_stage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n low tide:\n text: low tide\n ebb tide:\n text: ebb tide\n flood tide:\n text: flood tide\n high tide:\n text: high tide\n\nURI: TillageEnum
"},{"location":"TillageEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description drill None cutting disc None ridge till None strip tillage None zonal tillage None chisel None tined None mouldboard None disc plough None"},{"location":"TillageEnum/#slots","title":"Slots","text":"Name Description tillage Note method(s) used for tilling"},{"location":"TillageEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TillageEnum/#schema-source","title":"Schema Source","text":"name: tillage_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n drill:\n text: drill\n cutting disc:\n text: cutting disc\n ridge till:\n text: ridge till\n strip tillage:\n text: strip tillage\n zonal tillage:\n text: zonal tillage\n chisel:\n text: chisel\n tined:\n text: tined\n mouldboard:\n text: mouldboard\n disc plough:\n text: disc plough\n\nA time object represents a (local) time of day, independent of any particular day
URI: xsd:time
base: XSDTime
uri: xsd:time
repr: str
A value that is a timestamp. The range should be ISO-8601
URI: nmdc:TimestampValue
classDiagram\n class TimestampValue\n click TimestampValue href \"../TimestampValue\"\n AttributeValue <|-- TimestampValue\n click AttributeValue href \"../AttributeValue\"\n\n\n\n TimestampValue : has_raw_value\n\n TimestampValue : type\n\n\n\nname: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nclass_uri: nmdc:TimestampValue\n\nname: TimestampValue\ndescription: A value that is a timestamp. The range should be ISO-8601\nnotes:\n- 'removed the following slots: year, month, day'\nfrom_schema: https://w3id.org/nmdc/nmdc\nis_a: AttributeValue\nattributes:\n has_raw_value:\n name: has_raw_value\n description: The value that was specified for an annotation in raw form, i.e.\n a string. E.g. \"2 cm\" or \"2-4 cm\"\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_raw_value\n owner: TimestampValue\n domain_of:\n - AttributeValue\n range: string\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: TimestampValue\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:TimestampValue\n\nURI: TrainLineEnum
"},{"location":"TrainLineEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description red None green None orange None"},{"location":"TrainLineEnum/#slots","title":"Slots","text":"Name Description train_line The subway line name"},{"location":"TrainLineEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainLineEnum/#schema-source","title":"Schema Source","text":"name: train_line_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n red:\n text: red\n green:\n text: green\n orange:\n text: orange\n\nURI: TrainStatLocEnum
"},{"location":"TrainStatLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description south station above ground None south station underground None south station amtrak None forest hills None riverside None"},{"location":"TrainStatLocEnum/#slots","title":"Slots","text":"Name Description train_stat_loc The train station collection location"},{"location":"TrainStatLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStatLocEnum/#schema-source","title":"Schema Source","text":"name: train_stat_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n south station above ground:\n text: south station above ground\n south station underground:\n text: south station underground\n south station amtrak:\n text: south station amtrak\n forest hills:\n text: forest hills\n riverside:\n text: riverside\n\nURI: TrainStopLocEnum
"},{"location":"TrainStopLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description end None mid None downtown None"},{"location":"TrainStopLocEnum/#slots","title":"Slots","text":"Name Description train_stop_loc The train stop collection location"},{"location":"TrainStopLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"TrainStopLocEnum/#schema-source","title":"Schema Source","text":"name: train_stop_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n end:\n text: end\n mid:\n text: mid\n downtown:\n text: downtown\n\nURI: xsd:string
base: str
uri: xsd:string
a complete URI
URI: xsd:anyURI
base: URI
uri: xsd:anyURI
repr: str
a URI or a CURIE
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
URI: VisMediaEnum
"},{"location":"VisMediaEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description photos None videos None commonly of the building None site context (adjacent buildings, vegetation, terrain, streets) None interiors None equipment None 3D scans None"},{"location":"VisMediaEnum/#slots","title":"Slots","text":"Name Description vis_media The building visual media"},{"location":"VisMediaEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"VisMediaEnum/#schema-source","title":"Schema Source","text":"name: vis_media_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n photos:\n text: photos\n videos:\n text: videos\n commonly of the building:\n text: commonly of the building\n site context (adjacent buildings, vegetation, terrain, streets):\n text: site context (adjacent buildings, vegetation, terrain, streets)\n interiors:\n text: interiors\n equipment:\n text: equipment\n 3D scans:\n text: 3D scans\n\nURI: WallConstTypeEnum
"},{"location":"WallConstTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description frame construction None joisted masonry None light noncombustible None masonry noncombustible None modified fire resistive None fire resistive None"},{"location":"WallConstTypeEnum/#slots","title":"Slots","text":"Name Description wall_const_type The building class of the wall defined by the composition of the building ele..."},{"location":"WallConstTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallConstTypeEnum/#schema-source","title":"Schema Source","text":"name: wall_const_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n frame construction:\n text: frame construction\n joisted masonry:\n text: joisted masonry\n light noncombustible:\n text: light noncombustible\n masonry noncombustible:\n text: masonry noncombustible\n modified fire resistive:\n text: modified fire resistive\n fire resistive:\n text: fire resistive\n\nURI: WallFinishMatEnum
"},{"location":"WallFinishMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description plaster None gypsum plaster None veneer plaster None gypsum board None tile None terrazzo None stone facing None acoustical treatment None wood None metal None masonry None"},{"location":"WallFinishMatEnum/#slots","title":"Slots","text":"Name Description wall_finish_mat The material utilized to finish the outer most layer of the wall"},{"location":"WallFinishMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallFinishMatEnum/#schema-source","title":"Schema Source","text":"name: wall_finish_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n plaster:\n text: plaster\n gypsum plaster:\n text: gypsum plaster\n veneer plaster:\n text: veneer plaster\n gypsum board:\n text: gypsum board\n tile:\n text: tile\n terrazzo:\n text: terrazzo\n stone facing:\n text: stone facing\n acoustical treatment:\n text: acoustical treatment\n wood:\n text: wood\n metal:\n text: metal\n masonry:\n text: masonry\n\nURI: WallLocEnum
"},{"location":"WallLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WallLocEnum/#slots","title":"Slots","text":"Name Description wall_loc The relative location of the wall within the room"},{"location":"WallLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallLocEnum/#schema-source","title":"Schema Source","text":"name: wall_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: WallSurfTreatmentEnum
"},{"location":"WallSurfTreatmentEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description painted None wall paper None no treatment None paneling None stucco None fabric None"},{"location":"WallSurfTreatmentEnum/#slots","title":"Slots","text":"Name Description wall_surf_treatment The surface treatment of interior wall"},{"location":"WallSurfTreatmentEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallSurfTreatmentEnum/#schema-source","title":"Schema Source","text":"name: wall_surf_treatment_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n painted:\n text: painted\n wall paper:\n text: wall paper\n no treatment:\n text: no treatment\n paneling:\n text: paneling\n stucco:\n text: stucco\n fabric:\n text: fabric\n\nURI: WallTextureEnum
"},{"location":"WallTextureEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description crows feet None crows-foot stomp None None double skip None hawk and trowel None knockdown None popcorn None orange peel None rosebud stomp None Santa-Fe texture None skip trowel None smooth None stomp knockdown None swirl None"},{"location":"WallTextureEnum/#slots","title":"Slots","text":"Name Description wall_texture The feel, appearance, or consistency of a wall surface"},{"location":"WallTextureEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WallTextureEnum/#schema-source","title":"Schema Source","text":"name: wall_texture_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n crows feet:\n text: crows feet\n crows-foot stomp:\n text: crows-foot stomp\n ? ''\n : text: ''\n double skip:\n text: double skip\n hawk and trowel:\n text: hawk and trowel\n knockdown:\n text: knockdown\n popcorn:\n text: popcorn\n orange peel:\n text: orange peel\n rosebud stomp:\n text: rosebud stomp\n Santa-Fe texture:\n text: Santa-Fe texture\n skip trowel:\n text: skip trowel\n smooth:\n text: smooth\n stomp knockdown:\n text: stomp knockdown\n swirl:\n text: swirl\n\nURI: WaterFeatTypeEnum
"},{"location":"WaterFeatTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description fountain None pool None standing feature None stream None waterfall None"},{"location":"WaterFeatTypeEnum/#slots","title":"Slots","text":"Name Description water_feat_type The type of water feature present within the building being sampled"},{"location":"WaterFeatTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WaterFeatTypeEnum/#schema-source","title":"Schema Source","text":"name: water_feat_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n fountain:\n text: fountain\n pool:\n text: pool\n standing feature:\n text: standing feature\n stream:\n text: stream\n waterfall:\n text: waterfall\n\nURI: WeekdayEnum
"},{"location":"WeekdayEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description Monday None Tuesday None Wednesday None Thursday None Friday None Saturday None Sunday None"},{"location":"WeekdayEnum/#slots","title":"Slots","text":"Name Description weekday The day of the week when sampling occurred"},{"location":"WeekdayEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WeekdayEnum/#schema-source","title":"Schema Source","text":"name: weekday_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n Monday:\n text: Monday\n Tuesday:\n text: Tuesday\n Wednesday:\n text: Wednesday\n Thursday:\n text: Thursday\n Friday:\n text: Friday\n Saturday:\n text: Saturday\n Sunday:\n text: Sunday\n\nURI: WindowCondEnum
"},{"location":"WindowCondEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description damaged None needs repair None new None rupture None visible wear None"},{"location":"WindowCondEnum/#slots","title":"Slots","text":"Name Description window_cond The physical condition of the window at the time of sampling"},{"location":"WindowCondEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCondEnum/#schema-source","title":"Schema Source","text":"name: window_cond_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n damaged:\n text: damaged\n needs repair:\n text: needs repair\n new:\n text: new\n rupture:\n text: rupture\n visible wear:\n text: visible wear\n\nURI: WindowCoverEnum
"},{"location":"WindowCoverEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description blinds None curtains None none None"},{"location":"WindowCoverEnum/#slots","title":"Slots","text":"Name Description window_cover The type of window covering"},{"location":"WindowCoverEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowCoverEnum/#schema-source","title":"Schema Source","text":"name: window_cover_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n blinds:\n text: blinds\n curtains:\n text: curtains\n none:\n text: none\n\nURI: WindowHorizPosEnum
"},{"location":"WindowHorizPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description left None middle None right None"},{"location":"WindowHorizPosEnum/#slots","title":"Slots","text":"Name Description window_horiz_pos The horizontal position of the window on the wall"},{"location":"WindowHorizPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowHorizPosEnum/#schema-source","title":"Schema Source","text":"name: window_horiz_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n left:\n text: left\n middle:\n text: middle\n right:\n text: right\n\nURI: WindowLocEnum
"},{"location":"WindowLocEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description north None south None east None west None"},{"location":"WindowLocEnum/#slots","title":"Slots","text":"Name Description window_loc The relative location of the window within the room"},{"location":"WindowLocEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowLocEnum/#schema-source","title":"Schema Source","text":"name: window_loc_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n north:\n text: north\n south:\n text: south\n east:\n text: east\n west:\n text: west\n\nURI: WindowMatEnum
"},{"location":"WindowMatEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description clad None fiberglass None metal None vinyl None wood None"},{"location":"WindowMatEnum/#slots","title":"Slots","text":"Name Description window_mat The type of material used to finish a window"},{"location":"WindowMatEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowMatEnum/#schema-source","title":"Schema Source","text":"name: window_mat_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n clad:\n text: clad\n fiberglass:\n text: fiberglass\n metal:\n text: metal\n vinyl:\n text: vinyl\n wood:\n text: wood\n\nURI: WindowTypeEnum
"},{"location":"WindowTypeEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description single-hung sash window None horizontal sash window None fixed window None"},{"location":"WindowTypeEnum/#slots","title":"Slots","text":"Name Description window_type The type of windows"},{"location":"WindowTypeEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowTypeEnum/#schema-source","title":"Schema Source","text":"name: window_type_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n single-hung sash window:\n text: single-hung sash window\n horizontal sash window:\n text: horizontal sash window\n fixed window:\n text: fixed window\n\nURI: WindowVertPosEnum
"},{"location":"WindowVertPosEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description bottom None middle None top None low None high None"},{"location":"WindowVertPosEnum/#slots","title":"Slots","text":"Name Description window_vert_pos The vertical position of the window on the wall"},{"location":"WindowVertPosEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"WindowVertPosEnum/#schema-source","title":"Schema Source","text":"name: window_vert_pos_enum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n bottom:\n text: bottom\n middle:\n text: middle\n top:\n text: top\n low:\n text: low\n high:\n text: high\n\nRepresents an instance of an execution of a particular workflow
Note
This is an abstract class and should not be instantiated directly.
URI: nmdc:WorkflowExecution
Note
Mermaid class diagram too large to render.
"},{"location":"WorkflowExecution/#inheritance","title":"Inheritance","text":"name: WorkflowExecution\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An analysis contains secondary analysis results derived from sequence\n reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) subclasses of WorkflowExecution is a distinct\n run with start and stop times, potentially with different inputs and outputs\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: PlannedProcess\nabstract: true\nslots:\n- ended_at_time\n- execution_resource\n- git_url\n- started_at_time\n- version\n- was_informed_by\nslot_usage:\n started_at_time:\n name: started_at_time\n required: true\n git_url:\n name: git_url\n required: true\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n execution_resource:\n name: execution_resource\n required: true\n was_informed_by:\n name: was_informed_by\n required: true\nclass_uri: nmdc:WorkflowExecution\nrules:\n- preconditions:\n slot_conditions:\n qc_status:\n name: qc_status\n equals_string: pass\n postconditions:\n slot_conditions:\n has_output:\n name: has_output\n required: true\n description: If qc_status has a value of pass, then the has_output slot is required.\n title: qc_status_pass_has_output_required\n- preconditions:\n slot_conditions:\n qc_status:\n name: qc_status\n value_presence: ABSENT\n postconditions:\n slot_conditions:\n has_output:\n name: has_output\n required: true\n description: If qc_status is not specified, then the has_output slot is required.\n title: qc_status_pass_null_has_output_required\n\nname: WorkflowExecution\ndescription: Represents an instance of an execution of a particular workflow\nalt_descriptions:\n embl.ena:\n source: embl.ena\n description: An analysis contains secondary analysis results derived from sequence\n reads (e.g. a genome assembly)\ncomments:\n- Each instance of this (and all other) subclasses of WorkflowExecution is a distinct\n run with start and stop times, potentially with different inputs and outputs\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- analysis\nis_a: PlannedProcess\nabstract: true\nslot_usage:\n started_at_time:\n name: started_at_time\n required: true\n git_url:\n name: git_url\n required: true\n has_input:\n name: has_input\n required: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n execution_resource:\n name: execution_resource\n required: true\n was_informed_by:\n name: was_informed_by\n required: true\nattributes:\n ended_at_time:\n name: ended_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:endedAtTime\n rank: 1000\n alias: ended_at_time\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: string\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n execution_resource:\n name: execution_resource\n description: The computing resource or facility where the workflow was executed.\n examples:\n - value: NERSC-Cori\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: execution_resource\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: ExecutionResourceEnum\n required: true\n git_url:\n name: git_url\n description: The url that points to the exact github location of a workflow.\n examples:\n - value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n - value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: git_url\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n started_at_time:\n name: started_at_time\n notes:\n - 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\n from_schema: https://w3id.org/nmdc/nmdc\n mappings:\n - prov:startedAtTime\n rank: 1000\n alias: started_at_time\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: string\n required: true\n pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n version:\n name: version\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: version\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: string\n was_informed_by:\n name: was_informed_by\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n mappings:\n - prov:wasInformedBy\n rank: 1000\n alias: was_informed_by\n owner: WorkflowExecution\n domain_of:\n - WorkflowExecution\n range: DataGeneration\n required: true\n has_input:\n name: has_input\n description: An input to a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - input\n rank: 1000\n alias: has_input\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: NamedThing\n required: true\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n has_output:\n name: has_output\n description: An output from a process.\n from_schema: https://w3id.org/nmdc/nmdc\n aliases:\n - output\n rank: 1000\n alias: has_output\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: NamedThing\n multivalued: true\n structured_pattern:\n syntax: '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'\n interpolated: true\n processing_institution:\n name: processing_institution\n description: The organization that processed the sample.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: processing_institution\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: ProcessingInstitutionEnum\n protocol_link:\n name: protocol_link\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: protocol_link\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n - Study\n range: Protocol\n start_date:\n name: start_date\n description: The date on which any process or activity was started\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: start_date\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: string\n end_date:\n name: end_date\n description: The date on which any process or activity was ended\n todos:\n - add date string validation pattern\n comments:\n - We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n - The date should be formatted as YYYY-MM-DD\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: end_date\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: string\n qc_status:\n name: qc_status\n description: Stores information about the result of a process (ie the process\n of sequencing a library may have for qc_status of 'fail' if not enough data\n was generated)\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_status\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: StatusEnum\n qc_comment:\n name: qc_comment\n description: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed.\n (ie Failed at call-stage due to a malformed fastq file).\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: qc_comment\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: string\n has_failure_categorization:\n name: has_failure_categorization\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: has_failure_categorization\n owner: WorkflowExecution\n domain_of:\n - PlannedProcess\n range: FailureCategorization\n multivalued: true\n inlined: true\n inlined_as_list: true\n id:\n name: id\n description: A unique identifier for a thing. Must be either a CURIE shorthand\n for a URI or a complete URI\n notes:\n - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n - minting authority shoulders should probably be enumerated and checked in the\n pattern\n examples:\n - value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\n from_schema: https://w3id.org/nmdc/nmdc\n structured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n identifier: true\n alias: id\n owner: WorkflowExecution\n domain_of:\n - NamedThing\n range: uriorcurie\n required: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n name:\n name: name\n description: A human readable label for an entity\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: name\n owner: WorkflowExecution\n domain_of:\n - PersonValue\n - NamedThing\n - Protocol\n range: string\n description:\n name: description\n description: a human-readable description of a thing\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n slot_uri: dcterms:description\n alias: description\n owner: WorkflowExecution\n domain_of:\n - ImageValue\n - NamedThing\n range: string\n alternative_identifiers:\n name: alternative_identifiers\n description: A list of alternative identifiers for the entity.\n from_schema: https://w3id.org/nmdc/nmdc\n rank: 1000\n alias: alternative_identifiers\n owner: WorkflowExecution\n domain_of:\n - MetaboliteIdentification\n - NamedThing\n range: uriorcurie\n multivalued: true\n pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n type:\n name: type\n description: the class_uri of the class that has been instantiated\n notes:\n - replaces legacy nmdc:type slot\n - makes it easier to read example data files\n - required for polymorphic MongoDB collections\n examples:\n - value: nmdc:Biosample\n - value: nmdc:Study\n from_schema: https://w3id.org/nmdc/nmdc\n see_also:\n - https://github.com/microbiomedata/nmdc-schema/issues/1048\n - https://github.com/microbiomedata/nmdc-schema/issues/1233\n - https://github.com/microbiomedata/nmdc-schema/issues/248\n structured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n rank: 1000\n slot_uri: rdf:type\n designates_type: true\n alias: type\n owner: WorkflowExecution\n domain_of:\n - EukEval\n - FunctionalAnnotationAggMember\n - PeptideQuantification\n - ProteinQuantification\n - MobilePhaseSegment\n - PortionOfSubstance\n - MagBin\n - MetaboliteIdentification\n - GenomeFeature\n - FunctionalAnnotation\n - AttributeValue\n - NamedThing\n - OntologyRelation\n - FailureCategorization\n - Protocol\n - CreditAssociation\n - Doi\n range: uriorcurie\n required: true\nclass_uri: nmdc:WorkflowExecution\nrules:\n- preconditions:\n slot_conditions:\n qc_status:\n name: qc_status\n equals_string: pass\n postconditions:\n slot_conditions:\n has_output:\n name: has_output\n required: true\n description: If qc_status has a value of pass, then the has_output slot is required.\n title: qc_status_pass_has_output_required\n- preconditions:\n slot_conditions:\n qc_status:\n name: qc_status\n value_presence: ABSENT\n postconditions:\n slot_conditions:\n has_output:\n name: has_output\n required: true\n description: If qc_status is not specified, then the has_output slot is required.\n title: qc_status_pass_null_has_output_required\n\nreplaces DnaDnaseEnum and DnaseRnaEnum
URI: YesNoEnum
"},{"location":"YesNoEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description no None yes None"},{"location":"YesNoEnum/#slots","title":"Slots","text":"Name Description dna_dnase dnase_rna"},{"location":"YesNoEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"YesNoEnum/#schema-source","title":"Schema Source","text":"name: YesNoEnum\ndescription: replaces DnaDnaseEnum and DnaseRnaEnum\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\npermissible_values:\n 'no':\n text: 'no'\n 'yes':\n text: 'yes'\n\nThe work conducted by the National Microbiome Data Collaborative (https://ror.org/05cwx3318) is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (BER) under contract numbers DE-AC02-05CH11231 (LBNL), 89233218CNA000001 (LANL), and DE-AC05-76RL01830 (PNNL).
"},{"location":"about/#framework","title":"Framework","text":"This schema was made using the LinkML framework. LinkML is a data modeling language that is used to create data models in a human-readable format. The LinkML framework is used to generate the schema in multiple formats, including JSON-LD, YAML, and RDF.
NMDC uses the LinkML framework to create a schema to be used by researchers, data scientists, and developers to understand the structure of the data and how it is related.
"},{"location":"about/#citing-nmdc","title":"Citing NMDC","text":""},{"location":"about/#schema","title":"Schema","text":"Microbiome Data Coordination Center. (n.d.). NMDC Schema. GitHub. from https://github.com/microbiomedata/nmdc-schema
"},{"location":"about/#program-launch","title":"Program Launch","text":"E. M. Wood-Charlson, Anubhav, D. Auberry, H. Blanco, M. I. Borkum, Y. E. Corilo, K. W. Davenport, S. Deshpande, R. Devarakonda, M. Drake, W. D. Duncan, M. C. Flynn, D. Hays, B. Hu, M. Huntemann, P.-E. Li, M. Lipton, C.-C. Lo, D. Millard, K. Miller, P. D. Piehowski, S. Purvine, T. B. K. Reddy, M. Shakya, J. C. Sundaramurthi, P. Vangay, Y. Wei, B. E. Wilson, S. Canon, P. S. G. Chain, K. Fagnan, S. Martin, L. A. McCue, C. J. Mungall, N. J. Mouncey, M. E. Maxon, E. A. Eloe-Fadrosh, The National Microbiome Data Collaborative: enabling microbiome science. Nature Reviews Microbiology 18, 313-314 (2020). doi: 10.1038/s41579-020-0377-0
"},{"location":"abs_air_humidity/","title":"Slot: absolute air humidity (abs_air_humidity)","text":"Actual mass of water vapor - mh20 - present in the air water vapor mixture
URI: MIXS:0000122
"},{"location":"abs_air_humidity/#inheritance","title":"Inheritance","text":"name: abs_air_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram, kilogram per kilogram, kilogram, pound\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Actual mass of water vapor - mh20 - present in the air water vapor mixture\ntitle: absolute air humidity\nexamples:\n- value: 9 gram per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- absolute air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000122\nalias: abs_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe date on which the information was added to the database.
URI: nmdc:add_date
"},{"location":"add_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Biosample Biological source material which can be characterized by an experiment no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"add_date/#properties","title":"Properties","text":"name: add_date\ndescription: The date on which the information was added to the database.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: add_date\ndomain_of:\n- Biosample\n- DataGeneration\nrange: string\n\nAdditional (i.e. Secondary, tertiary, etc.) recovery methods deployed for increase of hydrocarbon recovery from resource and start date for each one of them. If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0001009
"},{"location":"add_recov_method/#inheritance","title":"Inheritance","text":"name: add_recov_method\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Additional (i.e. Secondary, tertiary, etc.) recovery methods deployed\n for increase of hydrocarbon recovery from resource and start date for each one of\n them. If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: secondary and tertiary recovery methods and start date\nexamples:\n- value: Polymer Addition;2018-06-21T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary and tertiary recovery methods and start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001009\nalias: add_recov_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation that doesn't fit anywhere else. Can also be used to propose new entries for fields with controlled vocabulary
URI: MIXS:0000300
"},{"location":"additional_info/#inheritance","title":"Inheritance","text":"name: additional_info\nannotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information that doesn't fit anywhere else. Can also be used to propose\n new entries for fields with controlled vocabulary\ntitle: additional info\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- additional info\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000300\nalias: additional_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe street name and building number where the sampling occurred.
URI: MIXS:0000218
"},{"location":"address/#inheritance","title":"Inheritance","text":"name: address\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The street name and building number where the sampling occurred.\ntitle: address\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- address\nrank: 1000\nis_a: core field\nstring_serialization: '{integer}{text}'\nslot_uri: MIXS:0000218\nalias: address\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of rooms (room number, room name) immediately adjacent to the sampling room
URI: MIXS:0000219
"},{"location":"adj_room/#inheritance","title":"Inheritance","text":"name: adj_room\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of rooms (room number, room name) immediately adjacent to the sampling\n room\ntitle: adjacent rooms\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- adjacent rooms\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000219\nalias: adj_room\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nAerospace structures typically consist of thin plates with stiffeners for the external surfaces, bulkheads and frames to support the shape and fasteners such as welds, rivets, screws and bolts to hold the components together
URI: MIXS:0000773
"},{"location":"aero_struc/#inheritance","title":"Inheritance","text":"name: aero_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Aerospace structures typically consist of thin plates with stiffeners\n for the external surfaces, bulkheads and frames to support the shape and fasteners\n such as welds, rivets, screws and bolts to hold the components together\ntitle: aerospace structure\nexamples:\n- value: plane\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aerospace structure\nrank: 1000\nis_a: core field\nstring_serialization: '[plane|glider]'\nslot_uri: MIXS:0000773\nalias: aero_struc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nAddition of fertilizers, pesticides, etc. - amount and time of applications
URI: MIXS:0000639
"},{"location":"agrochem_addition/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: agrochem_addition\nannotations:\n expected_value:\n tag: expected_value\n value: agrochemical name;agrochemical amount;timestamp\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Addition of fertilizers, pesticides, etc. - amount and time of applications\ntitle: history/agrochemical additions\nexamples:\n- value: roundup;5 milligram per liter;2018-06-21\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/agrochemical additions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{timestamp}'\nslot_uri: MIXS:0000639\nalias: agrochem_addition\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM
URI: MIXS:0000108
"},{"location":"air_PM_concen/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: air_PM_concen\nannotations:\n expected_value:\n tag: expected_value\n value: particulate matter name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrograms per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances that remain suspended in the air, and comprise\n mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple\n PM's by entering numeric values preceded by name of PM\ntitle: air particulate matter concentration\nexamples:\n- value: PM2.5;10 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air particulate matter concentration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000108\nalias: air_PM_concen\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTemperature of the air at the time of sampling
URI: MIXS:0000124
"},{"location":"air_temp/#inheritance","title":"Inheritance","text":"name: air_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature of the air at the time of sampling\ntitle: air temperature\nexamples:\n- value: 20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000124\nalias: air_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving an exposure to varying temperatures; should include the temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include different temperature regimens
URI: MIXS:0000551
"},{"location":"air_temp_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: air_temp_regm\nannotations:\n expected_value:\n tag: expected_value\n value: temperature value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to varying temperatures;\n should include the temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include different temperature regimens\ntitle: air temperature regimen\nexamples:\n- value: 25 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- air temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000551\nalias: air_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAluminum saturation (esp. For tropical soils)
URI: MIXS:0000607
"},{"location":"al_sat/#inheritance","title":"Inheritance","text":"name: al_sat\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Aluminum saturation (esp. For tropical soils)\ntitle: extreme_unusual_properties/Al saturation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000607\nalias: al_sat\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining Al saturation
URI: MIXS:0000324
"},{"location":"al_sat_meth/#inheritance","title":"Inheritance","text":"name: al_sat_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or URL\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining Al saturation\ntitle: extreme_unusual_properties/Al saturation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/Al saturation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000324\nalias: al_sat_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nAlkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate
URI: MIXS:0000421
"},{"location":"alkalinity/#inheritance","title":"Inheritance","text":"name: alkalinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliequivalent per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Alkalinity, the ability of a solution to neutralize acids to the equivalence\n point of carbonate or bicarbonate\ntitle: alkalinity\nexamples:\n- value: 50 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000421\nalias: alkalinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMethod used for alkalinity measurement
URI: MIXS:0000298
"},{"location":"alkalinity_method/#inheritance","title":"Inheritance","text":"name: alkalinity_method\nannotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method used for alkalinity measurement\ntitle: alkalinity method\nexamples:\n- value: titration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkalinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000298\nalias: alkalinity_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of alkyl diethers
URI: MIXS:0000490
"},{"location":"alkyl_diethers/#inheritance","title":"Inheritance","text":"name: alkyl_diethers\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of alkyl diethers\ntitle: alkyl diethers\nexamples:\n- value: 0.005 mole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- alkyl diethers\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000490\nalias: alkyl_diethers\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nthe list of protein identifiers that are associated with the peptide sequence
URI: nmdc:all_proteins
","text":""},{"location":"all_proteins/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"all_proteins/#properties","title":"Properties","text":"Range: GeneProduct
Multivalued: True
name: all_proteins\ndescription: the list of protein identifiers that are associated with the peptide\n sequence\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: all_proteins\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\nmultivalued: true\n\nAltitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth's surface. In this context, the altitude measurement is the vertical distance between the earth's surface above sea level and the sampled position in the air
URI: MIXS:0000094
"},{"location":"alt/#inheritance","title":"Inheritance","text":"name: alt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: Altitude is a term used to identify heights of objects such as airplanes,\n space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric\n layers and clouds. It is used to measure the height of an object which is above\n the earth's surface. In this context, the altitude measurement is the vertical distance\n between the earth's surface above sea level and the sampled position in the air\ntitle: altitude\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- altitude\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000094\nalias: alt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nA list of alternative descriptions for the entity. The distinction between description and alternative descriptions is application-specific.
URI: nmdc:alternative_descriptions
"},{"location":"alternative_descriptions/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_descriptions/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_descriptions\ndescription: A list of alternative descriptions for the entity. The distinction between\n description and alternative descriptions is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternative_descriptions\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\nA list of alternative identifiers for the entity.
URI: nmdc:alternative_identifiers
"},{"location":"alternative_identifiers/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$
name: alternative_identifiers\ndescription: A list of alternative identifiers for the entity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: alternative_identifiers\ndomain_of:\n- MetaboliteIdentification\n- NamedThing\nrange: uriorcurie\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,\\(\\)\\=\\#]*$\n\nA list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.
URI: nmdc:alternative_names
"},{"location":"alternative_names/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes ChemicalEntity An atom or molecule that can be represented with a chemical formula no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no OrthologyGroup A set of genes or gene products in which all members are orthologous no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no EnvironmentalMaterialTerm no OntologyClass A representation of class defined in an external ontology no"},{"location":"alternative_names/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_names\ndescription: A list of alternative names used to refer to the entity. The distinction\n between name and alternative names is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\n- skos:altLabel\nrank: 1000\nalias: alternative_names\ndomain_of:\n- OntologyClass\n- Study\nrange: string\nmultivalued: true\n\nA list of alternative titles for the entity. The distinction between title and alternative titles is application-specific.
URI: nmdc:alternative_titles
"},{"location":"alternative_titles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"alternative_titles/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: alternative_titles\ndescription: A list of alternative titles for the entity. The distinction between\n title and alternative titles is application-specific.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:alternative\nrank: 1000\nalias: alternative_titles\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\nMeasurement of aminopeptidase activity
URI: MIXS:0000172
"},{"location":"aminopept_act/#inheritance","title":"Inheritance","text":"name: aminopept_act\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of aminopeptidase activity\ntitle: aminopeptidase activity\nexamples:\n- value: 0.269 mole per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aminopeptidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000172\nalias: aminopept_act\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of ammonium in the sample
URI: MIXS:0000427
"},{"location":"ammonium/#inheritance","title":"Inheritance","text":"name: ammonium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ammonium in the sample\ntitle: ammonium\nexamples:\n- value: 1.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ammonium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000427\nalias: ammonium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of ammonium nitrogen in the sample
URI: nmdc:ammonium_nitrogen
"},{"location":"ammonium_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ammonium_nitrogen/#properties","title":"Properties","text":"name: ammonium_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ammonium nitrogen in the sample\ntitle: ammonium nitrogen\nexamples:\n- value: 2.3 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- ammonium_nitrogen\n- NH4-N\nrank: 1000\nalias: ammonium_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe unit of illuminance and luminous emittance, measuring luminous flux per unit area
URI: MIXS:0000140
"},{"location":"amount_light/#inheritance","title":"Inheritance","text":"name: amount_light\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux, lumens per square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The unit of illuminance and luminous emittance, measuring luminous flux\n per unit area\ntitle: amount of light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount of light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000140\nalias: amount_light\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:analysis_identifiers
"},{"location":"analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: analysis_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nSelect all the data types associated or available for this biosample
URI: nmdc:analysis_type
"},{"location":"analysis_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"analysis_type/#properties","title":"Properties","text":"Range: AnalysisTypeEnum
Multivalued: True
Recommended: True
name: analysis_type\ndescription: Select all the data types associated or available for this biosample\ntitle: analysis/data type\nexamples:\n- value: metagenomics; metabolomics; metaproteomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIxS:investigation_type\nrank: 3\nalias: analysis_type\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: AnalysisTypeEnum\nrecommended: true\nmultivalued: true\n\nThe type of analyte(s) that were measured in the data generation process and analyzed
_ in the Workflow Chain_
__
URI: nmdc:analyte_category
"},{"location":"analyte_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"analyte_category/#properties","title":"Properties","text":"Range: String
Required: True
name: analyte_category\ndescription: \"The type of analyte(s) that were measured in the data generation process\\\n \\ and analyzed\\n in the Workflow Chain\\n\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: analyte_category\ndomain_of:\n- DataGeneration\nrange: string\nrequired: true\n\nInformation about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B)
URI: MIXS:0000247
"},{"location":"ances_data/#inheritance","title":"Inheritance","text":"name: ances_data\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about either pedigree or other ancestral information description\n (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A\n x B) x B] x B)\ntitle: ancestral data\nexamples:\n- value: A/3*B\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ancestral data\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000247\nalias: ances_data\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.
URI: MIXS:0000644
"},{"location":"annual_precpt/#inheritance","title":"Inheritance","text":"name: annual_precpt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of all annual precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean annual precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000644\nalias: annual_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMean annual temperature
URI: MIXS:0000642
"},{"location":"annual_temp/#inheritance","title":"Inheritance","text":"name: annual_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Mean annual temperature\ntitle: mean annual temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean annual temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000642\nalias: annual_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple antibiotic regimens
URI: MIXS:0000553
"},{"location":"antibiotic_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: antibiotic_regm\nannotations:\n expected_value:\n tag: expected_value\n value: antibiotic name;antibiotic amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving antibiotic administration; should\n include the name of antibiotic, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple antibiotic regimens\ntitle: antibiotic regimen\nexamples:\n- value: penicillin;5 milligram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- antibiotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000553\nalias: antibiotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAPI gravity is a measure of how heavy or light a petroleum liquid is compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e API)
URI: MIXS:0000157
"},{"location":"api/#inheritance","title":"Inheritance","text":"name: api\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degrees API\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'API gravity is a measure of how heavy or light a petroleum liquid is\n compared to water (source: https://en.wikipedia.org/wiki/API_gravity) (e.g. 31.1\u00ac\u221e\n API)'\ntitle: API gravity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- API gravity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000157\nalias: api\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:applied_roles
"},{"location":"applied_roles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applied_roles/#properties","title":"Properties","text":"Range: CreditEnum
Multivalued: True
Required: True
name: applied_roles\nannotations:\n tooltip:\n tag: tooltip\n value: 'Identify all CRediT roles associated with this contributor. CRediT Information:\n https://info.orcid.org/credit-for-research-contribution ; CRediT: https://credit.niso.org/'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: applied_roles\ndomain_of:\n- CreditAssociation\nrange: CreditEnum\nrequired: true\nmultivalued: true\n\nURI: nmdc:applies_to_person
"},{"location":"applies_to_person/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CreditAssociation This class supports binding associated researchers to studies no"},{"location":"applies_to_person/#properties","title":"Properties","text":"Range: PersonValue
Required: True
name: applies_to_person\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: applies_to_person\ndomain_of:\n- CreditAssociation\nrange: PersonValue\nrequired: true\n\nAn architectural structure is a human-made, free-standing, immobile outdoor construction
URI: MIXS:0000774
"},{"location":"arch_struc/#inheritance","title":"Inheritance","text":"name: arch_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: An architectural structure is a human-made, free-standing, immobile outdoor\n construction\ntitle: architectural structure\nexamples:\n- value: shed\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- architectural structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000774\nalias: arch_struc\ndomain_of:\n- Biosample\nrange: arch_struc_enum\nmultivalued: false\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000133
"},{"location":"aromatics_pc/#inheritance","title":"Inheritance","text":"name: aromatics_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: aromatics wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- aromatics wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000133\nalias: aromatics_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA score for comparing metagenomic assembly quality from same sample.
URI: nmdc:asm_score
"},{"location":"asm_score/#inheritance","title":"Inheritance","text":"name: asm_score\ndescription: A score for comparing metagenomic assembly quality from same sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: asm_score\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000135
"},{"location":"asphaltenes_pc/#inheritance","title":"Inheritance","text":"name: asphaltenes_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: asphaltenes wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- asphaltenes wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000135\nalias: asphaltenes_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:assembly_identifiers
"},{"location":"assembly_identifiers/#inheritance","title":"Inheritance","text":"name: assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: assembly_identifiers\nrange: string\n\nA list of DOIs associated with a resource, such as a list of DOIS associated with a Study.
URI: nmdc:associated_dois
"},{"location":"associated_dois/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"associated_dois/#properties","title":"Properties","text":"Range: Doi
Multivalued: True
name: associated_dois\ndescription: A list of DOIs associated with a resource, such as a list of DOIS associated\n with a Study.\nexamples:\n- value: '[{''doi'': ''doi:10.46936/intm.proj.2021.60141/60000423'', ''doi_provider'':\n ''emsl'', ''doi_category'': ''award_doi''}, {''doi'': ''doi:10.1101/2022.12.12.520098'',\n ''doi_category'': ''publication_doi''}, {''doi'': ''doi:10.48321/D1Z60Q'', ''doi_category'':\n ''data_management_plan_doi'', ''doi_provider'': ''gsc''}]'\n description: Provides a list of two DOIs; specifically, an EMSL award DOI and a\n publication DOI.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Associated DOIs\n- Associated digital object identifiers\nrank: 1000\nalias: associated_dois\ndomain_of:\n- Study\nrange: Doi\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe study associated with a resource.
URI: nmdc:associated_studies
"},{"location":"associated_studies/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Biosample Biological source material which can be characterized by an experiment yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"associated_studies/#properties","title":"Properties","text":"Range: Study
Multivalued: True
Required: True
name: associated_studies\ndescription: The study associated with a resource.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: associated_studies\ndomain_of:\n- Biosample\n- DataGeneration\nrange: Study\nrequired: true\nmultivalued: true\nstructured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\n\nMeasurement of atmospheric data; can include multiple data
URI: MIXS:0001097
"},{"location":"atmospheric_data/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: atmospheric_data\nannotations:\n expected_value:\n tag: expected_value\n value: atmospheric data name;measurement value\n occurrence:\n tag: occurrence\n value: m\ndescription: Measurement of atmospheric data; can include multiple data\ntitle: atmospheric data\nexamples:\n- value: wind speed;9 knots\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- atmospheric data\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0001097\nalias: atmospheric_data\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe average of dew point measures taken at the beginning of every hour over a 24 hour period on the sampling day
URI: MIXS:0000141
"},{"location":"avg_dew_point/#inheritance","title":"Inheritance","text":"name: avg_dew_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of dew point measures taken at the beginning of every hour\n over a 24 hour period on the sampling day\ntitle: average dew point\nexamples:\n- value: 25.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000141\nalias: avg_dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDaily average occupancy of room. Indicate the number of person(s) daily occupying the sampling room.
URI: MIXS:0000775
"},{"location":"avg_occup/#inheritance","title":"Inheritance","text":"name: avg_occup\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Daily average occupancy of room. Indicate the number of person(s) daily\n occupying the sampling room.\ntitle: average daily occupancy\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average daily occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000775\nalias: avg_occup\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe average of temperatures taken at the beginning of every hour over a 24 hour period on the sampling day
URI: MIXS:0000142
"},{"location":"avg_temp/#inheritance","title":"Inheritance","text":"name: avg_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of temperatures taken at the beginning of every hour over\n a 24 hour period on the sampling day\ntitle: average temperature\nexamples:\n- value: 12.5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- average temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000142\nalias: avg_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nBacterial production in the water column measured by isotope uptake
URI: MIXS:0000683
"},{"location":"bac_prod/#inheritance","title":"Inheritance","text":"name: bac_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Bacterial production in the water column measured by isotope uptake\ntitle: bacterial production\nexamples:\n- value: 5 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000683\nalias: bac_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of bacterial respiration in the water column
URI: MIXS:0000684
"},{"location":"bac_resp/#inheritance","title":"Inheritance","text":"name: bac_resp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, micromole oxygen per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of bacterial respiration in the water column\ntitle: bacterial respiration\nexamples:\n- value: 300 micromole oxygen per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial respiration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000684\nalias: bac_resp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of bacterial carbon production
URI: MIXS:0000173
"},{"location":"bacteria_carb_prod/#inheritance","title":"Inheritance","text":"name: bacteria_carb_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of bacterial carbon production\ntitle: bacterial carbon production\nexamples:\n- value: 2.53 microgram per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bacterial carbon production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000173\nalias: bacteria_carb_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nForce per unit area exerted against a surface by the weight of air above that surface
URI: MIXS:0000096
"},{"location":"barometric_press/#inheritance","title":"Inheritance","text":"name: barometric_press\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millibar\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Force per unit area exerted against a surface by the weight of air above\n that surface\ntitle: barometric pressure\nexamples:\n- value: 5 millibar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- barometric pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000096\nalias: barometric_press\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nName of the basin (e.g. Campos)
URI: MIXS:0000290
"},{"location":"basin/#inheritance","title":"Inheritance","text":"name: basin\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the basin (e.g. Campos)\ntitle: basin name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- basin name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000290\nalias: basin\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe number of bathrooms in the building
URI: MIXS:0000776
"},{"location":"bathroom_count/#inheritance","title":"Inheritance","text":"name: bathroom_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of bathrooms in the building\ntitle: bathroom count\nexamples:\n- value: '1'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bathroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000776\nalias: bathroom_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe number of bedrooms in the building
URI: MIXS:0000777
"},{"location":"bedroom_count/#inheritance","title":"Inheritance","text":"name: bedroom_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of bedrooms in the building\ntitle: bedroom count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bedroom count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000777\nalias: bedroom_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of benzene in the sample
URI: MIXS:0000153
"},{"location":"benzene/#inheritance","title":"Inheritance","text":"name: benzene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of benzene in the sample\ntitle: benzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- benzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000153\nalias: benzene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nthe specific protein identifier most correctly associated with the peptide sequence
URI: nmdc:best_protein
","text":""},{"location":"best_protein/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"best_protein/#properties","title":"Properties","text":"name: best_protein\ndescription: the specific protein identifier most correctly associated with the peptide\n sequence\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: best_protein\ndomain_of:\n- PeptideQuantification\n- ProteinQuantification\nrange: GeneProduct\n\nName of the metagenome-assembled genome.
URI: nmdc:bin_name
"},{"location":"bin_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_name/#properties","title":"Properties","text":"Range: String
Required: True
name: bin_name\ndescription: Name of the metagenome-assembled genome.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_name\ndomain_of:\n- MagBin\nrange: string\nrequired: true\n\nThe quality of the metagenome-assembled genome based on MIMAG standards (https://doi.org/10.1038/nbt.3893).
URI: nmdc:bin_quality
"},{"location":"bin_quality/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"bin_quality/#properties","title":"Properties","text":"name: bin_quality\ndescription: The quality of the metagenome-assembled genome based on MIMAG standards\n (https://doi.org/10.1038/nbt.3893).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bin_quality\ndomain_of:\n- MagBin\nrange: BinQualityEnum\n\nNumber of contigs that ended up in a medium or high quality bin.
URI: nmdc:binned_contig_num
"},{"location":"binned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"binned_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: binned_contig_num\ndescription: Number of contigs that ended up in a medium or high quality bin.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: binned_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nAmount of dissolved oxygen needed by aerobic biological organisms in a body of water to break down organic material present in a given water sample at certain temperature over a specific time period
URI: MIXS:0000653
"},{"location":"biochem_oxygen_dem/#inheritance","title":"Inheritance","text":"name: biochem_oxygen_dem\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Amount of dissolved oxygen needed by aerobic biological organisms in\n a body of water to break down organic material present in a given water sample at\n certain temperature over a specific time period\ntitle: biochemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biochemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000653\nalias: biochem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nList of biocides (commercial name of product and supplier) and date of administration
URI: MIXS:0001011
"},{"location":"biocide/#inheritance","title":"Inheritance","text":"name: biocide\nannotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of biocides (commercial name of product and supplier) and date of\n administration\ntitle: biocide administration\nexamples:\n- value: ALPHA 1427;Baker Hughes;2008-01-23\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001011\nalias: biocide\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMethod of biocide administration (dose, frequency, duration, time elapsed between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)
URI: MIXS:0000456
"},{"location":"biocide_admin_method/#inheritance","title":"Inheritance","text":"name: biocide_admin_method\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method of biocide administration (dose, frequency, duration, time elapsed\n between last biociding and sampling) (e.g. 150 mg/l; weekly; 4 hr; 3 days)\ntitle: biocide administration method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biocide administration method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration}'\nslot_uri: MIXS:0000456\nalias: biocide_admin_method\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:biogas_retention_time
"},{"location":"biogas_retention_time/#properties","title":"Properties","text":"name: biogas_retention_time\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_retention_time\nrange: string\n\nURI: nmdc:biogas_temperature
"},{"location":"biogas_temperature/#properties","title":"Properties","text":"name: biogas_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biogas_temperature\nrange: string\n\nThe level of genome modification.
URI: MIXS:0000858
"},{"location":"biol_stat/#inheritance","title":"Inheritance","text":"name: biol_stat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The level of genome modification.\ntitle: biological status\nexamples:\n- value: natural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biological status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000858\nalias: biol_stat\ndomain_of:\n- Biosample\nrange: biol_stat_enum\nmultivalued: false\n\nAmount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements
URI: MIXS:0000174
"},{"location":"biomass/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: biomass\nannotations:\n expected_value:\n tag: expected_value\n value: biomass type;measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n e.g. Microbial, total. Can include multiple measurements\ntitle: biomass\nexamples:\n- value: total;20 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biomass\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000174\nalias: biomass\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:biomaterial_purity
"},{"location":"biomaterial_purity/#inheritance","title":"Inheritance","text":"name: biomaterial_purity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biomaterial_purity\ndomain_of:\n- ProcessedSample\nrange: QuantityValue\n\nURI: nmdc:biosample_categories
"},{"location":"biosample_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"biosample_categories/#properties","title":"Properties","text":"Range: BiosampleCategoryEnum
Multivalued: True
name: biosample_categories\ntitle: Categories the biosample belongs to\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: biosample_categories\ndomain_of:\n- Biosample\nrange: BiosampleCategoryEnum\nmultivalued: true\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:biosample_identifiers
"},{"location":"biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: biosample_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThis property links a database object to the set of samples within it.
URI: nmdc:biosample_set
"},{"location":"biosample_set/#inheritance","title":"Inheritance","text":"Range: Biosample
Multivalued: True
name: biosample_set\ndescription: This property links a database object to the set of samples within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: biosample_set\ndomain_of:\n- Database\nrange: Biosample\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nInformation about treatment(s) involving use of biotic factors, such as bacteria, viruses or fungi.
URI: MIXS:0001038
"},{"location":"biotic_regm/#inheritance","title":"Inheritance","text":"name: biotic_regm\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about treatment(s) involving use of biotic factors, such\n as bacteria, viruses or fungi.\ntitle: biotic regimen\nexamples:\n- value: sample inoculated with Rhizobium spp. Culture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- biotic regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001038\nalias: biotic_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDescription of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object
URI: MIXS:0000028
"},{"location":"biotic_relationship/#inheritance","title":"Inheritance","text":"name: biotic_relationship\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\ndescription: Description of relationship(s) between the subject organism and other\n organism(s) it is associated with. E.g., parasite on species X; mutualist with species\n Y. The target organism is the subject of the relationship, and the other organism(s)\n is the object\ntitle: observed biotic relationship\nexamples:\n- value: free living\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed biotic relationship\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000028\nalias: biotic_relationship\ndomain_of:\n- Biosample\nrange: biotic_relationship_enum\nmultivalued: false\n\nConcentration of bishomohopanol
URI: MIXS:0000175
"},{"location":"bishomohopanol/#inheritance","title":"Inheritance","text":"name: bishomohopanol\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, microgram per gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of bishomohopanol\ntitle: bishomohopanol\nexamples:\n- value: 14 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bishomohopanol\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000175\nalias: bishomohopanol\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nResting diastolic blood pressure, measured as mm mercury
URI: MIXS:0000258
"},{"location":"blood_press_diast/#inheritance","title":"Inheritance","text":"name: blood_press_diast\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Resting diastolic blood pressure, measured as mm mercury\ntitle: host blood pressure diastolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure diastolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000258\nalias: blood_press_diast\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nResting systolic blood pressure, measured as mm mercury
URI: MIXS:0000259
"},{"location":"blood_press_syst/#inheritance","title":"Inheritance","text":"name: blood_press_syst\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter mercury\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Resting systolic blood pressure, measured as mm mercury\ntitle: host blood pressure systolic\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host blood pressure systolic\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000259\nalias: blood_press_syst\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of bromide
URI: MIXS:0000176
"},{"location":"bromide/#inheritance","title":"Inheritance","text":"name: bromide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of bromide\ntitle: bromide\nexamples:\n- value: 0.05 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- bromide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000176\nalias: bromide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe building design, construction and operation documents
URI: MIXS:0000787
"},{"location":"build_docs/#inheritance","title":"Inheritance","text":"name: build_docs\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building design, construction and operation documents\ntitle: design, construction, and operation documents\nexamples:\n- value: maintenance plans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- design, construction, and operation documents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000787\nalias: build_docs\ndomain_of:\n- Biosample\nrange: build_docs_enum\nmultivalued: false\n\nThe primary function for which a building or discrete part of a building is intended to be used
URI: MIXS:0000761
"},{"location":"build_occup_type/#inheritance","title":"Inheritance","text":"Range: BuildOccupTypeEnum
Multivalued: True
name: build_occup_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: The primary function for which a building or discrete part of a building\n is intended to be used\ntitle: building occupancy type\nexamples:\n- value: market\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building occupancy type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000761\nalias: build_occup_type\ndomain_of:\n- Biosample\nrange: build_occup_type_enum\nmultivalued: true\n\nA location (geography) where a building is set
URI: MIXS:0000768
"},{"location":"building_setting/#inheritance","title":"Inheritance","text":"name: building_setting\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A location (geography) where a building is set\ntitle: building setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- building setting\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000768\nalias: building_setting\ndomain_of:\n- Biosample\nrange: building_setting_enum\nmultivalued: false\n\nThe age of the built structure since construction
URI: MIXS:0000145
"},{"location":"built_struc_age/#inheritance","title":"Inheritance","text":"name: built_struc_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The age of the built structure since construction\ntitle: built structure age\nexamples:\n- value: '15'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000145\nalias: built_struc_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe characterization of the location of the built structure as high or low human density
URI: MIXS:0000778
"},{"location":"built_struc_set/#inheritance","title":"Inheritance","text":"name: built_struc_set\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The characterization of the location of the built structure as high or\n low human density\ntitle: built structure setting\nexamples:\n- value: rural\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure setting\nrank: 1000\nis_a: core field\nstring_serialization: '[urban|rural]'\nslot_uri: MIXS:0000778\nalias: built_struc_set\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA physical structure that is a body or assemblage of bodies in space to form a system capable of supporting loads
URI: MIXS:0000721
"},{"location":"built_struc_type/#inheritance","title":"Inheritance","text":"name: built_struc_type\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A physical structure that is a body or assemblage of bodies in space\n to form a system capable of supporting loads\ntitle: built structure type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- built structure type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000721\nalias: built_struc_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nElectrical conductivity is a measure of the ability to carry electric current, which is mostly dictated by the chemistry of and amount of water.
URI: nmdc:bulk_elect_conductivity
"},{"location":"bulk_elect_conductivity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"bulk_elect_conductivity/#properties","title":"Properties","text":"name: bulk_elect_conductivity\ndescription: Electrical conductivity is a measure of the ability to carry electric\n current, which is mostly dictated by the chemistry of and amount of water.\ntitle: bulk electrical conductivity\ncomments:\n- Provide the value output of the field instrument.\nexamples:\n- value: JsonObj(has_raw_value='0.017 mS/cm', has_numeric_value=0.017, has_unit='mS/cm')\n description: The conductivity measurement was 0.017 millisiemens per centimeter.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: bulk_elect_conductivity\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of calcium in the sample
URI: MIXS:0000432
"},{"location":"calcium/#inheritance","title":"Inheritance","text":"name: calcium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of calcium in the sample\ntitle: calcium\nexamples:\n- value: 0.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- calcium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000432\nalias: calcium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nthe file containing calibration data object
URI: nmdc:calibration_object
"},{"location":"calibration_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process no"},{"location":"calibration_object/#properties","title":"Properties","text":"name: calibration_object\ndescription: the file containing calibration data object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_object\ndomain_of:\n- CalibrationInformation\nrange: DataObject\nstructured_pattern:\n syntax: '{id_nmdc_prefix}:dobj-{id_shoulder}-{id_blade}$'\n interpolated: true\n\nThis property links a database object to the set of calibrations within it.
URI: nmdc:calibration_set
"},{"location":"calibration_set/#inheritance","title":"Inheritance","text":"Range: CalibrationInformation
Multivalued: True
name: calibration_set\ndescription: This property links a database object to the set of calibrations within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: calibration_set\ndomain_of:\n- Database\nrange: CalibrationInformation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nthe reference standard(s) used for calibration
URI: nmdc:calibration_standard
"},{"location":"calibration_standard/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process no"},{"location":"calibration_standard/#properties","title":"Properties","text":"name: calibration_standard\ndescription: the reference standard(s) used for calibration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_standard\ndomain_of:\n- CalibrationInformation\nrange: CalibrationStandardEnum\n\nthe target measurement of the calibration
URI: nmdc:calibration_target
"},{"location":"calibration_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process yes"},{"location":"calibration_target/#properties","title":"Properties","text":"name: calibration_target\ndescription: the target measurement of the calibration\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: calibration_target\ndomain_of:\n- CalibrationInformation\nrange: CalibrationTargetEnum\n\nCarbon dioxide (gas) amount or concentration at the time of sampling
URI: MIXS:0000097
"},{"location":"carb_dioxide/#inheritance","title":"Inheritance","text":"name: carb_dioxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Carbon dioxide (gas) amount or concentration at the time of sampling\ntitle: carbon dioxide\nexamples:\n- value: 410 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000097\nalias: carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCarbon monoxide (gas) amount or concentration at the time of sampling
URI: MIXS:0000098
"},{"location":"carb_monoxide/#inheritance","title":"Inheritance","text":"name: carb_monoxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Carbon monoxide (gas) amount or concentration at the time of sampling\ntitle: carbon monoxide\nexamples:\n- value: 0.1 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon monoxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000098\nalias: carb_monoxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nRatio of amount or concentrations of carbon to nitrogen
URI: MIXS:0000310
"},{"location":"carb_nitro_ratio/#inheritance","title":"Inheritance","text":"name: carb_nitro_ratio\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ratio of amount or concentrations of carbon to nitrogen\ntitle: carbon/nitrogen ratio\nexamples:\n- value: '0.417361111'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- carbon/nitrogen ratio\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000310\nalias: carb_nitro_ratio\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe area of the ceiling space within the room
URI: MIXS:0000148
"},{"location":"ceil_area/#inheritance","title":"Inheritance","text":"name: ceil_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The area of the ceiling space within the room\ntitle: ceiling area\nexamples:\n- value: 25 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000148\nalias: ceil_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000779
"},{"location":"ceil_cond/#inheritance","title":"Inheritance","text":"name: ceil_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the ceiling at the time of sampling; photos\n or video preferred; use drawings to indicate location of damaged areas\ntitle: ceiling condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000779\nalias: ceil_cond\ndomain_of:\n- Biosample\nrange: ceil_cond_enum\nmultivalued: false\n\nThe type of material used to finish a ceiling
URI: MIXS:0000780
"},{"location":"ceil_finish_mat/#inheritance","title":"Inheritance","text":"name: ceil_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material used to finish a ceiling\ntitle: ceiling finish material\nexamples:\n- value: stucco\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000780\nalias: ceil_finish_mat\ndomain_of:\n- Biosample\nrange: ceil_finish_mat_enum\nmultivalued: false\n\nThe construction format of the ceiling
URI: MIXS:0000782
"},{"location":"ceil_struc/#inheritance","title":"Inheritance","text":"name: ceil_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The construction format of the ceiling\ntitle: ceiling structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling structure\nrank: 1000\nis_a: core field\nstring_serialization: '[wood frame|concrete]'\nslot_uri: MIXS:0000782\nalias: ceil_struc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe feel, appearance, or consistency of a ceiling surface
URI: MIXS:0000783
"},{"location":"ceil_texture/#inheritance","title":"Inheritance","text":"name: ceil_texture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The feel, appearance, or consistency of a ceiling surface\ntitle: ceiling texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000783\nalias: ceil_texture\ndomain_of:\n- Biosample\nrange: ceil_texture_enum\nmultivalued: false\n\nThe ability of the ceiling to provide inertia against temperature fluctuations. Generally this means concrete that is exposed. A metal deck that supports a concrete slab will act thermally as long as it is exposed to room air flow
URI: MIXS:0000143
"},{"location":"ceil_thermal_mass/#inheritance","title":"Inheritance","text":"name: ceil_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the ceiling to provide inertia against temperature fluctuations.\n Generally this means concrete that is exposed. A metal deck that supports a concrete\n slab will act thermally as long as it is exposed to room air flow\ntitle: ceiling thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000143\nalias: ceil_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of ceiling according to the ceiling's appearance or construction
URI: MIXS:0000784
"},{"location":"ceil_type/#inheritance","title":"Inheritance","text":"name: ceil_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of ceiling according to the ceiling's appearance or construction\ntitle: ceiling type\nexamples:\n- value: coffered\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000784\nalias: ceil_type\ndomain_of:\n- Biosample\nrange: ceil_type_enum\nmultivalued: false\n\nSigns of the presence of mold or mildew on the ceiling
URI: MIXS:0000781
"},{"location":"ceil_water_mold/#inheritance","title":"Inheritance","text":"name: ceil_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the ceiling\ntitle: ceiling signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ceiling signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000781\nalias: ceil_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. For chemical entities of biological interest ontology (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
URI: MIXS:0000751
"},{"location":"chem_administration/#inheritance","title":"Inheritance","text":"Range: ControlledTermValue
Multivalued: True
name: chem_administration\nannotations:\n expected_value:\n tag: expected_value\n value: CHEBI;timestamp\n occurrence:\n tag: occurrence\n value: m\ndescription: List of chemical compounds administered to the host or site where sampling\n occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple\n compounds. For chemical entities of biological interest ontology (chebi) (v 163),\n http://purl.bioontology.org/ontology/chebi\ntitle: chemical administration\nexamples:\n- value: agar [CHEBI:2509];2018-05-11T20:00Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical administration\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]};{timestamp}'\nslot_uri: MIXS:0000751\nalias: chem_administration\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTreatment involving use of mutagens; should include the name of mutagen, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mutagen regimens
URI: MIXS:0000555
"},{"location":"chem_mutagen/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: chem_mutagen\nannotations:\n expected_value:\n tag: expected_value\n value: mutagen name;mutagen amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving use of mutagens; should include the name of mutagen,\n amount administered, treatment regimen including how many times the treatment was\n repeated, how long each treatment lasted, and the start and end time of the entire\n treatment; can include multiple mutagen regimens\ntitle: chemical mutagen\nexamples:\n- value: nitrous acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical mutagen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000555\nalias: chem_mutagen\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA measure of the capacity of water to consume oxygen during the decomposition of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite
URI: MIXS:0000656
"},{"location":"chem_oxygen_dem/#inheritance","title":"Inheritance","text":"name: chem_oxygen_dem\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A measure of the capacity of water to consume oxygen during the decomposition\n of organic matter and the oxidation of inorganic chemicals such as ammonia and nitrite\ntitle: chemical oxygen demand\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical oxygen demand\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000656\nalias: chem_oxygen_dem\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMethod of chemical administration(dose, frequency, duration, time elapsed between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)
URI: MIXS:0000457
"},{"location":"chem_treat_method/#inheritance","title":"Inheritance","text":"name: chem_treat_method\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;frequency;duration;duration\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Method of chemical administration(dose, frequency, duration, time elapsed\n between administration and sampling) (e.g. 50 mg/l; twice a week; 1 hr; 0 days)\ntitle: chemical treatment method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment method\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration};{duration};{duration}'\nslot_uri: MIXS:0000457\nalias: chem_treat_method\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nList of chemical compounds administered upstream the sampling location where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors, demulsifiers, and other production chemicals etc.). The commercial name of the product and name of the supplier should be provided. The date of administration should also be included
URI: MIXS:0001012
"},{"location":"chem_treatment/#inheritance","title":"Inheritance","text":"name: chem_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: name;name;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of chemical compounds administered upstream the sampling location\n where sampling occurred (e.g. Glycols, H2S scavenger, corrosion and scale inhibitors,\n demulsifiers, and other production chemicals etc.). The commercial name of the product\n and name of the supplier should be provided. The date of administration should also\n be included\ntitle: chemical treatment\nexamples:\n- value: ACCENT 1125;DOW;2010-11-17\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chemical treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text};{timestamp}'\nslot_uri: MIXS:0001012\nalias: chem_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe type of chemical conversion process.
URI: nmdc:chemical_conversion_category
"},{"location":"chemical_conversion_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no"},{"location":"chemical_conversion_category/#properties","title":"Properties","text":"name: chemical_conversion_category\ndescription: The type of chemical conversion process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_conversion_category\ndomain_of:\n- ChemicalConversionProcess\nrange: ChemicalConversionCategoryEnum\n\nThis property links a database object to the set of chemical entities within it.
URI: nmdc:chemical_entity_set
","text":""},{"location":"chemical_entity_set/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: chemical_entity_set\ndescription: This property links a database object to the set of chemical entities\n within it.\ndeprecated: Deprecation of the ChemicalEntity class, means deprecation of the chemical_entity_set\n as well.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: chemical_entity_set\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA generic grouping for molecular formulae and empirical formulae
URI: nmdc:chemical_formula
"},{"location":"chemical_formula/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no"},{"location":"chemical_formula/#properties","title":"Properties","text":"name: chemical_formula\ndescription: A generic grouping for molecular formulae and empirical formulae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chemical_formula\ndomain_of:\n- ChemicalEntity\nrange: string\n\nTool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.
URI: MIXS:0000052
"},{"location":"chimera_check/#inheritance","title":"Inheritance","text":"name: chimera_check\nannotations:\n expected_value:\n tag: expected_value\n value: name and version of software, parameters used\ndescription: Tool(s) used for chimera checking, including version number and parameters,\n to discover and remove chimeric sequences. A chimeric sequence is comprised of two\n or more phylogenetically distinct parent sequences.\ntitle: chimera check software\nexamples:\n- value: uchime;v4.1;default parameters\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chimera check software\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{software};{version};{parameters}'\nslot_uri: MIXS:0000052\nalias: chimera_check\nrange: TextValue\nmultivalued: false\n\nConcentration of chloride in the sample
URI: MIXS:0000429
"},{"location":"chloride/#inheritance","title":"Inheritance","text":"name: chloride\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of chloride in the sample\ntitle: chloride\nexamples:\n- value: 5000 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chloride\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000429\nalias: chloride\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of chlorophyll
URI: MIXS:0000177
"},{"location":"chlorophyll/#inheritance","title":"Inheritance","text":"name: chlorophyll\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter, microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of chlorophyll\ntitle: chlorophyll\nexamples:\n- value: 5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- chlorophyll\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000177\nalias: chlorophyll\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of chromatography used in a process.
URI: nmdc:chromatographic_category
"},{"location":"chromatographic_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no"},{"location":"chromatographic_category/#properties","title":"Properties","text":"name: chromatographic_category\ndescription: The type of chromatography used in a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: chromatographic_category\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: ChromatographicCategoryEnum\n\nTreatment involving an exposure to a particular climate; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple climates
URI: MIXS:0001040
"},{"location":"climate_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: climate_environment\nannotations:\n expected_value:\n tag: expected_value\n value: climate name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to a particular climate; treatment regimen\n including how many times the treatment was repeated, how long each treatment lasted,\n and the start and end time of the entire treatment; can include multiple climates\ntitle: climate environment\nexamples:\n- value: tropical climate;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- climate environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001040\nalias: climate_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nNMDC Schema is a collaborative, multidisciplinary project that seeks to harmonize data across the microbiome research community. We welcome any and all kinds of contributions. Our goal is to make it easy for you to contribute to the project, and to make sure that your contributions are properly reviewed and integrated.
"},{"location":"collaboration/#how-can-i-contribute","title":"How can I contribute?","text":"We welcome any and all kinds of contribution, including:
Please see our Contributing Guidelines for more information on how to contribute to the project, and our Code of Conduct for information on how to interact with the community.
"},{"location":"collaboration/#how-do-i-do-x-why-doesnt-y-work-where-can-i-go-to-get-help","title":"How do I do X? Why doesn\u2019t Y work? Where can I go to get help?","text":"First, please check if your question is answered on the FAQ and or in this documentation. We always welcome questions, bug reports, feature requests, and feedback via our GitHub issue tracker:
https://github.com/microbiomedata/nmdc-schema/issues
"},{"location":"collaboration/#how-do-i-run-a-collaborative-schema-project","title":"How do I run a collaborative schema project?","text":"Please check some guidelines from LinkML Schema Developers: https://linkml.io/linkml/howtos/collaborative-development.html Consult NMDC Schema Contribution guidelines directly: GoogleSlides
"},{"location":"collected_from/","title":"Slot: collected_from","text":"The Site from which a Biosample was collected
URI: nmdc:collected_from
"},{"location":"collected_from/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment yes"},{"location":"collected_from/#properties","title":"Properties","text":"name: collected_from\ndescription: The Site from which a Biosample was collected\ntodos:\n- add an OBO slot_uri ?\ncomments:\n- this illustrates implementing a Biosample relation with a (binary) slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: collected_from\ndomain_of:\n- Biosample\nrange: FieldResearchSite\n\nURI: nmdc:collecting_biosamples_from_site_set
"},{"location":"collecting_biosamples_from_site_set/#inheritance","title":"Inheritance","text":"Range: CollectingBiosamplesFromSite
Multivalued: True
name: collecting_biosamples_from_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: collecting_biosamples_from_site_set\ndomain_of:\n- Database\nrange: CollectingBiosamplesFromSite\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant
URI: MIXS:0000011
"},{"location":"collection_date/#inheritance","title":"Inheritance","text":"name: collection_date\nannotations:\n expected_value:\n tag: expected_value\n value: date and time\ndescription: 'The time of sampling, either as an instance (single point in time) or\n interval. In case no exact time is available, the date/time can be right truncated\n i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;\n 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'\ntitle: collection date\nexamples:\n- value: 2018-05-11T10:00:00+01:00; 2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- collection date\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000011\nalias: collection_date\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nDate the incubation was harvested/collected/ended. Only relevant for incubation samples.
URI: nmdc:collection_date_inc
"},{"location":"collection_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_date_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_date_inc\ndescription: Date the incubation was harvested/collected/ended. Only relevant for\n incubation samples.\ntitle: incubation collection date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n all acceptable.\nexamples:\n- value: '2021-04-15'\n- value: 2021-04\n- value: '2021'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 2\nstring_serialization: '{date, arbitrary precision}'\nalias: collection_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nThe time of sampling, either as an instance (single point) or interval.
URI: nmdc:collection_time
"},{"location":"collection_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_time\ndescription: The time of sampling, either as an instance (single point) or interval.\ntitle: collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: '13:33'\n- value: '13:33:55'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 1\nstring_serialization: '{time, seconds optional}'\nalias: collection_time\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nTime the incubation was harvested/collected/ended. Only relevant for incubation samples.
URI: nmdc:collection_time_inc
"},{"location":"collection_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"collection_time_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: collection_time_inc\ndescription: Time the incubation was harvested/collected/ended. Only relevant for\n incubation samples.\ntitle: incubation collection time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: '13:33'\n- value: '13:33:55'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 3\nstring_serialization: '{time, seconds optional}'\nalias: collection_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nURI: nmdc:community
"},{"location":"community/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"community/#properties","title":"Properties","text":"name: community\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: community\ndomain_of:\n- Biosample\nrange: string\n\nEstimate of the completeness of the metagenome-assembled genome, estimated by a tool like CheckM.
URI: nmdc:completeness
"},{"location":"completeness/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no MagBin no"},{"location":"completeness/#properties","title":"Properties","text":"Range: Float
Minimum Value: 0
name: completeness\ndescription: Estimate of the completeness of the metagenome-assembled genome, estimated\n by a tool like CheckM.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completeness\ndomain_of:\n- EukEval\n- MagBin\nrange: float\nminimum_value: 0\n\nURI: nmdc:completion_date
"},{"location":"completion_date/#properties","title":"Properties","text":"name: completion_date\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: completion_date\nrange: string\n\nIf provided, specifies the compression type
URI: nmdc:compression_type
"},{"location":"compression_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"compression_type/#properties","title":"Properties","text":"name: compression_type\ndescription: If provided, specifies the compression type\ntodos:\n- consider setting the range to an enum\nexamples:\n- value: gzip\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: compression_type\ndomain_of:\n- DataObject\nrange: string\n\nThe concentration of a substance used in a process
URI: nmdc:concentration
"},{"location":"concentration/#inheritance","title":"Inheritance","text":"name: concentration\ndescription: The concentration of a substance used in a process\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: concentration\nrange: QuantityValue\n\nPreliminary treatment of either phase with a suitable solution of the other phase (in the absence of main extractable solute(s)) so that when the subsequent equilibration is carried out changes in the (volume) phase ratio or in the concentrations of other components are minimized.
URI: nmdc:conditionings
"},{"location":"conditionings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"conditionings/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: conditionings\ndescription: Preliminary treatment of either phase with a suitable solution of the\n other phase (in the absence of main extractable solute(s)) so that when the subsequent\n equilibration is carried out changes in the (volume) phase ratio or in the concentrations\n of other components are minimized.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: conditionings\ndomain_of:\n- FiltrationProcess\nrange: string\nmultivalued: true\n\nElectrical conductivity of water
URI: MIXS:0000692
"},{"location":"conduc/#inheritance","title":"Inheritance","text":"name: conduc\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliSiemens per centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Electrical conductivity of water\ntitle: conductivity\nexamples:\n- value: 10 milliSiemens per centimeter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- conductivity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000692\nalias: conduc\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThis property links a database object to the set of configurations within it.
URI: nmdc:configuration_set
"},{"location":"configuration_set/#inheritance","title":"Inheritance","text":"Range: Configuration
Multivalued: True
name: configuration_set\ndescription: This property links a database object to the set of configurations within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: configuration_set\ndomain_of:\n- Database\nrange: Configuration\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA type of container.
URI: nmdc:contained_in
"},{"location":"contained_in/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no StorageProcess A planned process with the objective to preserve and protect material entitie... no"},{"location":"contained_in/#properties","title":"Properties","text":"name: contained_in\ndescription: A type of container.\nexamples:\n- value: test tube\n- value: falcon tube\n- value: whirlpak\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contained_in\ndomain_of:\n- SubSamplingProcess\n- StorageProcess\nrange: ContainerCategoryEnum\n\nThe volume of the container an analyte is stored in or an activity takes place in
URI: nmdc:container_size
"},{"location":"container_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no FiltrationProcess The process of segregation of phases; e no"},{"location":"container_size/#properties","title":"Properties","text":"name: container_size\ndescription: The volume of the container an analyte is stored in or an activity takes\n place in\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: container_size\ndomain_of:\n- SubSamplingProcess\n- FiltrationProcess\nrange: QuantityValue\n\nEstimate of the completeness of the metagenome-assembled genome, estimated by a tool like CheckM.
URI: nmdc:contamination
"},{"location":"contamination/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no MagBin no"},{"location":"contamination/#properties","title":"Properties","text":"Range: Float
Minimum Value: 0
name: contamination\ndescription: Estimate of the completeness of the metagenome-assembled genome, estimated\n by a tool like CheckM.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: contamination\ndomain_of:\n- EukEval\n- MagBin\nrange: float\nminimum_value: 0\n\nTotal size in bp of all contigs.
URI: nmdc:contig_bp
"},{"location":"contig_bp/#inheritance","title":"Inheritance","text":"name: contig_bp\ndescription: Total size in bp of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contig_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sum of the (length*log(length)) of all contigs, times some constant. Increase the contiguity, the score will increase
URI: nmdc:contigs
"},{"location":"contigs/#inheritance","title":"Inheritance","text":"name: contigs\ndescription: The sum of the (length*log(length)) of all contigs, times some constant. Increase\n the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: contigs\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe cooling system identifier
URI: MIXS:0000785
"},{"location":"cool_syst_id/#inheritance","title":"Inheritance","text":"name: cool_syst_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The cooling system identifier\ntitle: cooling system identifier\nexamples:\n- value: '12345'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- cooling system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000785\nalias: cool_syst_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nbasic fields
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:core_field
"},{"location":"core_field/#inheritance","title":"Inheritance","text":"name: core field\ndescription: basic fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: core_field\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:count
"},{"location":"count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember yes"},{"location":"count/#properties","title":"Properties","text":"Range: Integer
Required: True
name: count\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: count\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: integer\nrequired: true\n\nWhether or not crop is rotated, and if yes, rotation schedule
URI: MIXS:0000318
"},{"location":"crop_rotation/#inheritance","title":"Inheritance","text":"name: crop_rotation\nannotations:\n expected_value:\n tag: expected_value\n value: crop rotation status;schedule\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Whether or not crop is rotated, and if yes, rotation schedule\ntitle: history/crop rotation\nexamples:\n- value: yes;R2/2017-01-01/2018-12-31/P6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/crop rotation\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000318\nalias: crop_rotation\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nGiven a set of contigs, the L50 is defined as the sequence length of the shortest contig at 50% of the total genome length.
URI: nmdc:ctg_l50
"},{"location":"ctg_l50/#inheritance","title":"Inheritance","text":"name: ctg_l50\ndescription: Given a set of contigs, the L50 is defined as the sequence length of\n the shortest contig at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs.
URI: nmdc:ctg_l90
"},{"location":"ctg_l90/#inheritance","title":"Inheritance","text":"name: ctg_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n length for which the collection of all contigs of that length or longer contains\n at least 90% of the sum of the lengths of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum contig length.
URI: nmdc:ctg_logsum
"},{"location":"ctg_logsum/#inheritance","title":"Inheritance","text":"name: ctg_logsum\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum contig length.
URI: nmdc:ctg_max
"},{"location":"ctg_max/#inheritance","title":"Inheritance","text":"name: ctg_max\ndescription: Maximum contig length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of contigs, each with its own length, the N50 count is defined as the smallest number_of_contigs whose length sum makes up half of genome size.
URI: nmdc:ctg_n50
"},{"location":"ctg_n50/#inheritance","title":"Inheritance","text":"name: ctg_n50\ndescription: Given a set of contigs, each with its own length, the N50 count is defined\n as the smallest number_of_contigs whose length sum makes up half of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of contigs, each with its own length, the N90 count is defined as the smallest number of contigs whose length sum makes up 90% of genome size.
URI: nmdc:ctg_n90
"},{"location":"ctg_n90/#inheritance","title":"Inheritance","text":"name: ctg_n90\ndescription: Given a set of contigs, each with its own length, the N90 count is defined\n as the smallest number of contigs whose length sum makes up 90% of genome size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nPowersum of all contigs is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
URI: nmdc:ctg_powsum
"},{"location":"ctg_powsum/#inheritance","title":"Inheritance","text":"name: ctg_powsum\ndescription: Powersum of all contigs is the same as logsum except that it uses the\n sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: ctg_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nName or reference for the hydroponic or in vitro culture rooting medium; can be the name of a commonly used medium or reference to a specific medium, e.g. Murashige and Skoog medium. If the medium has not been formally published, use the rooting medium descriptors.
URI: MIXS:0001041
"},{"location":"cult_root_med/#inheritance","title":"Inheritance","text":"name: cult_root_med\nannotations:\n expected_value:\n tag: expected_value\n value: name, PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name or reference for the hydroponic or in vitro culture rooting medium;\n can be the name of a commonly used medium or reference to a specific medium, e.g.\n Murashige and Skoog medium. If the medium has not been formally published, use the\n rooting medium descriptors.\ntitle: culture rooting medium\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- culture rooting medium\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001041\nalias: cult_root_med\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nPresent state of sample site
URI: MIXS:0001080
"},{"location":"cur_land_use/#inheritance","title":"Inheritance","text":"name: cur_land_use\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Present state of sample site\ntitle: current land use\nexamples:\n- value: conifers\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current land use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001080\nalias: cur_land_use\ndomain_of:\n- Biosample\nrange: cur_land_use_enum\nmultivalued: false\n\nVegetation classification from one or more standard classification systems, or agricultural crop
URI: MIXS:0000312
"},{"location":"cur_vegetation/#inheritance","title":"Inheritance","text":"name: cur_vegetation\nannotations:\n expected_value:\n tag: expected_value\n value: current vegetation type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Vegetation classification from one or more standard classification systems,\n or agricultural crop\ntitle: current vegetation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000312\nalias: cur_vegetation\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\nReference or method used in vegetation classification
URI: MIXS:0000314
"},{"location":"cur_vegetation_meth/#inheritance","title":"Inheritance","text":"name: cur_vegetation_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in vegetation classification\ntitle: current vegetation method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- current vegetation method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000314\nalias: cur_vegetation_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe category of the file, such as instrument data from data generation or processed data from a workflow execution.
URI: nmdc:data_category
"},{"location":"data_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_category/#properties","title":"Properties","text":"name: data_category\ndescription: The category of the file, such as instrument data from data generation\n or processed data from a workflow execution.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: data_category\ndomain_of:\n- DataObject\nrange: DataCategoryEnum\n\nThis property links a database object to the set of data generations within it.
URI: nmdc:data_generation_set
"},{"location":"data_generation_set/#inheritance","title":"Inheritance","text":"Range: DataGeneration
Multivalued: True
name: data_generation_set\ndescription: This property links a database object to the set of data generations\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: data_generation_set\ndomain_of:\n- Database\nrange: DataGeneration\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of data objects within it.
URI: nmdc:data_object_set
"},{"location":"data_object_set/#inheritance","title":"Inheritance","text":"Range: DataObject
Multivalued: True
name: data_object_set\ndescription: This property links a database object to the set of data objects within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: data_object_set\ndomain_of:\n- Database\nrange: DataObject\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe type of file represented by the data object.
URI: nmdc:data_object_type
"},{"location":"data_object_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"data_object_type/#properties","title":"Properties","text":"name: data_object_type\ndescription: The type of file represented by the data object.\nexamples:\n- value: FT ICR-MS Analysis Results\n- value: GC-MS Metabolomics Results\nfrom_schema: https://w3id.org/nmdc/nmdc\nstructured_aliases:\n data_object_type:\n literal_form: data_object_type\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\nrank: 1000\nalias: data_object_type\ndomain_of:\n- DataObject\nrange: FileTypeEnum\n\nfrom database class
URI: nmdc:date_created
"},{"location":"date_created/#properties","title":"Properties","text":"name: date_created\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: date_created\nrange: string\n\nThe date of the last time it rained
URI: MIXS:0000786
"},{"location":"date_last_rain/#inheritance","title":"Inheritance","text":"name: date_last_rain\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The date of the last time it rained\ntitle: date last rain\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- date last rain\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000786\nalias: date_last_rain\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nThe definition of the ontology term as provided by the ontology.
URI: nmdc:definition
"},{"location":"definition/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no OrthologyGroup A set of genes or gene products in which all members are orthologous no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no EnvironmentalMaterialTerm no OntologyClass A representation of class defined in an external ontology no"},{"location":"definition/#properties","title":"Properties","text":"name: definition\ndescription: The definition of the ontology term as provided by the ontology.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: definition\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: string\n\nDensity of the sample, which is its mass per unit volume (aka volumetric mass density)
URI: MIXS:0000435
"},{"location":"density/#inheritance","title":"Inheritance","text":"name: density\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter, gram per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Density of the sample, which is its mass per unit volume (aka volumetric\n mass density)\ntitle: density\nexamples:\n- value: 1000 kilogram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000435\nalias: density\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMain depositional environment (https://en.wikipedia.org/wiki/Depositional_environment). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000992
"},{"location":"depos_env/#inheritance","title":"Inheritance","text":"name: depos_env\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main depositional environment (https://en.wikipedia.org/wiki/Depositional_environment).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: depositional environment\nexamples:\n- value: Continental - Alluvial\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000992\nalias: depos_env\ndomain_of:\n- Biosample\nrange: depos_env_enum\nmultivalued: false\n\nThe vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.
URI: MIXS:0000018
"},{"location":"depth/#inheritance","title":"Inheritance","text":"name: depth\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: The vertical distance below local surface, e.g. for sediment or soil\n samples depth is measured from sediment or soil surface, respectively. Depth can\n be reported as an interval for subsurface samples.\ntitle: depth\nexamples:\n- value: 10 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000018\nalias: depth\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\na human-readable description of a thing
URI: dcterms:description
"},{"location":"description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MetabolomicsAnalysis no Study A study summarizes the overall goal of a research initiative and outlines the... yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no Site no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... no GeneProduct A molecule encoded by a gene that has an evolved function no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no CalibrationInformation A calibration object that is associated with a process no FiltrationProcess The process of segregation of phases; e no ImageValue An attribute value representing an image no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ProcessedSample no MetatranscriptomeAnnotation no Biosample Biological source material which can be characterized by an experiment no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no CollectingBiosamplesFromSite no MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no EnvironmentalMaterialTerm no MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... no Sample A sample is a material entity that can be characterized by an experiment no ChemicalEntity An atom or molecule that can be represented with a chemical formula no MaterialEntity no Instrument A material entity that is designed to perform a function in a scientific inve... no NamedThing a databased entity or concept/class no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no Manifest A qualified collection of DataObjects that can be analyzed together in the sa... no OrthologyGroup A set of genes or gene products in which all members are orthologous no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no OntologyClass A representation of class defined in an external ontology no Configuration A set of parameters that define the actions of a process and is shared among ... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no LibraryPreparation no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes DataObject An object that primarily consists of symbols that represent information yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"description/#properties","title":"Properties","text":"name: description\ndescription: a human-readable description of a thing\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: dcterms:description\nalias: description\ndomain_of:\n- ImageValue\n- NamedThing\nrange: string\n\nSome frequently asked questions about developing the NMDC Schema.
"},{"location":"developer-docs/#what-are-some-effective-strategies-for-collaborative-schema-development","title":"What are some effective strategies for collaborative schema development?","text":"LinkML Collaborative Development Google Slides Presentation
"},{"location":"developer-docs/#how-do-i-migrate-from-one-version-of-the-nmdc-schema-to-another","title":"How do I migrate from one version of the NMDC schema to another?","text":"Version 10 to 11 migration
"},{"location":"developer-docs/#how-do-i-view-the-nmdc-schema-programmatically","title":"How do I view the NMDC schema programmatically?","text":"NMDC SchemaView Documentation SchemaView Documentation
"},{"location":"dew_point/","title":"Slot: dew point (dew_point)","text":"The temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.
URI: MIXS:0000129
"},{"location":"dew_point/#inheritance","title":"Inheritance","text":"name: dew_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The temperature to which a given parcel of humid air must be cooled,\n at constant barometric pressure, for water vapor to condense into water.\ntitle: dew point\nexamples:\n- value: 22 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dew point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000129\nalias: dew_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of diether lipids; can include multiple types of diether lipids
URI: MIXS:0000178
"},{"location":"diether_lipids/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: diether_lipids\nannotations:\n expected_value:\n tag: expected_value\n value: diether lipid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: nanogram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of diether lipids; can include multiple types of diether\n lipids\ntitle: diether lipids\nexamples:\n- value: 0.2 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- diether lipids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000178\nalias: diether_lipids\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nWhen rendering information, this attribute to specify the order in which the information should be rendered.
URI: nmdc:display_order
"},{"location":"display_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ImageValue An attribute value representing an image no"},{"location":"display_order/#properties","title":"Properties","text":"name: display_order\ndescription: When rendering information, this attribute to specify the order in which\n the information should be rendered.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: display_order\ndomain_of:\n- ImageValue\nrange: integer\n\nConcentration of dissolved carbon dioxide in the sample or liquid portion of the sample
URI: MIXS:0000436
"},{"location":"diss_carb_dioxide/#inheritance","title":"Inheritance","text":"name: diss_carb_dioxide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved carbon dioxide in the sample or liquid portion\n of the sample\ntitle: dissolved carbon dioxide\nexamples:\n- value: 5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved carbon dioxide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000436\nalias: diss_carb_dioxide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved hydrogen
URI: MIXS:0000179
"},{"location":"diss_hydrogen/#inheritance","title":"Inheritance","text":"name: diss_hydrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved hydrogen\ntitle: dissolved hydrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved hydrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000179\nalias: diss_hydrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter
URI: MIXS:0000434
"},{"location":"diss_inorg_carb/#inheritance","title":"Inheritance","text":"name: diss_inorg_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Dissolved inorganic carbon concentration in the sample, typically measured\n after filtering the sample using a 0.45 micrometer filter\ntitle: dissolved inorganic carbon\nexamples:\n- value: 2059 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000434\nalias: diss_inorg_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved inorganic nitrogen
URI: MIXS:0000698
"},{"location":"diss_inorg_nitro/#inheritance","title":"Inheritance","text":"name: diss_inorg_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved inorganic nitrogen\ntitle: dissolved inorganic nitrogen\nexamples:\n- value: 761 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000698\nalias: diss_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved inorganic phosphorus in the sample
URI: MIXS:0000106
"},{"location":"diss_inorg_phosp/#inheritance","title":"Inheritance","text":"name: diss_inorg_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved inorganic phosphorus in the sample\ntitle: dissolved inorganic phosphorus\nexamples:\n- value: 56.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved inorganic phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000106\nalias: diss_inorg_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved iron in the sample
URI: MIXS:0000139
"},{"location":"diss_iron/#inheritance","title":"Inheritance","text":"name: diss_iron\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved iron in the sample\ntitle: dissolved iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000139\nalias: diss_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid
URI: MIXS:0000433
"},{"location":"diss_org_carb/#inheritance","title":"Inheritance","text":"name: diss_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved organic carbon in the sample, liquid portion\n of the sample, or aqueous phase of the fluid\ntitle: dissolved organic carbon\nexamples:\n- value: 197 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000433\nalias: diss_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2
URI: MIXS:0000162
"},{"location":"diss_org_nitro/#inheritance","title":"Inheritance","text":"name: diss_org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Dissolved organic nitrogen concentration measured as; total dissolved\n nitrogen - NH4 - NO3 - NO2\ntitle: dissolved organic nitrogen\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000162\nalias: diss_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved oxygen
URI: MIXS:0000119
"},{"location":"diss_oxygen/#inheritance","title":"Inheritance","text":"name: diss_oxygen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved oxygen\ntitle: dissolved oxygen\nexamples:\n- value: 175 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000119\nalias: diss_oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of dissolved oxygen in the oil field produced fluids as it contributes to oxgen-corrosion and microbial activity (e.g. Mic).
URI: MIXS:0000438
"},{"location":"diss_oxygen_fluid/#inheritance","title":"Inheritance","text":"name: diss_oxygen_fluid\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per kilogram, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of dissolved oxygen in the oil field produced fluids as\n it contributes to oxgen-corrosion and microbial activity (e.g. Mic).\ntitle: dissolved oxygen in fluids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- dissolved oxygen in fluids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000438\nalias: diss_oxygen_fluid\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\n260/280 measurement of DNA sample purity
URI: nmdc:dna_absorb1
"},{"location":"dna_absorb1/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: dna_absorb1\ndescription: 260/280 measurement of DNA sample purity\ntitle: DNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nis_a: biomaterial_purity\nalias: dna_absorb1\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\n260/230 measurement of DNA sample purity
URI: nmdc:dna_absorb2
"},{"location":"dna_absorb2/#inheritance","title":"Inheritance","text":"Range: Float
Recommended: True
name: dna_absorb2\ndescription: 260/230 measurement of DNA sample purity\ntitle: DNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nis_a: biomaterial_purity\nalias: dna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\n\nProvide information on the site your DNA sample was collected from
URI: nmdc:dna_collect_site
"},{"location":"dna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_collect_site/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_collect_site\ndescription: Provide information on the site your DNA sample was collected from\ntitle: DNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: dna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_concentration
"},{"location":"dna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProcessedSample no Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_concentration/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 2000
name: dna_concentration\ntitle: DNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nalias: dna_concentration\ndomain_of:\n- Biosample\n- ProcessedSample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\nTube or plate (96-well)
URI: nmdc:dna_cont_type
"},{"location":"dna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_type/#properties","title":"Properties","text":"Range: JgiContTypeEnum
Recommended: True
name: dna_cont_type\ndescription: Tube or plate (96-well)\ntitle: DNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: dna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: JgiContTypeEnum\nrecommended: true\n\nURI: nmdc:dna_cont_well
"},{"location":"dna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_cont_well/#properties","title":"Properties","text":"Range: String
Recommended: True
Regex pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
name: dna_cont_well\ntitle: DNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: dna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\npattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n\nURI: nmdc:dna_container_id
"},{"location":"dna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_container_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_container_id\ntitle: DNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: dna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_dnase
"},{"location":"dna_dnase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_dnase/#properties","title":"Properties","text":"Range: YesNoEnum
Recommended: True
name: dna_dnase\ntitle: DNase treatment DNA\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 13\nalias: dna_dnase\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: YesNoEnum\nrecommended: true\n\nDescribe the method/protocol/kit used to extract DNA/RNA.
URI: nmdc:dna_isolate_meth
"},{"location":"dna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_isolate_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: DNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Sample Isolation Method\nrank: 16\nstring_serialization: '{text}'\nalias: dna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nList any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.
URI: nmdc:dna_organisms
"},{"location":"dna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_organisms/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\ntitle: DNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: dna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_project_contact
"},{"location":"dna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_project_contact/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_project_contact\ntitle: DNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: dna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_samp_id
"},{"location":"dna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_samp_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_samp_id\ntitle: DNA sample ID\ntodos:\n- Removed identifier = TRUE from dna_samp_ID in JGI_sample_slots, as a class can't\n have two identifiers. How to force uniqueness? Moot because that column will be\n prefilled?\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: dna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nSolution in which the DNA sample has been suspended
URI: nmdc:dna_sample_format
"},{"location":"dna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_format/#properties","title":"Properties","text":"Range: DNASampleFormatEnum
Recommended: True
name: dna_sample_format\ndescription: Solution in which the DNA sample has been suspended\ntitle: DNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: dna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: DNASampleFormatEnum\nrecommended: true\n\nGive the DNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
URI: nmdc:dna_sample_name
"},{"location":"dna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_sample_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_sample_name\ndescription: Give the DNA sample a name that is meaningful to you. Sample names must\n be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: DNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: dna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project
"},{"location":"dna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project\ntitle: DNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Seq Project ID\nrank: 1\nstring_serialization: '{text}'\nalias: dna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project_name
"},{"location":"dna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project_name\ntitle: DNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: JGI Pond metagenomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: dna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_seq_project_pi
"},{"location":"dna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_seq_project_pi/#properties","title":"Properties","text":"Range: String
Recommended: True
name: dna_seq_project_pi\ntitle: DNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: dna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:dna_volume
"},{"location":"dna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dna_volume/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: dna_volume\ntitle: DNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n accepts values < 25, but JGI may refuse to process them unless permission has been\n granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: dna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nURI: nmdc:dnase_rna
"},{"location":"dnase_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"dnase_rna/#properties","title":"Properties","text":"Range: YesNoEnum
Recommended: True
name: dnase_rna\ntitle: DNase treated\ncomments:\n- Note DNase treatment is required for all RNA samples.\nexamples:\n- value: 'no'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Was Sample DNAse treated?\nrank: 13\nalias: dnase_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: YesNoEnum\nrecommended: true\n\nThe resource type the corresponding doi resolves to.
URI: nmdc:doi_category
"},{"location":"doi_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_category/#properties","title":"Properties","text":"Range: DoiCategoryEnum
Required: True
name: doi_category\ndescription: The resource type the corresponding doi resolves to.\nexamples:\n- value: dataset_doi\n description: The corresponding DOI is a dataset resource type.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: doi_category\ndomain_of:\n- Doi\nrange: DoiCategoryEnum\nrequired: true\n\nThe authority, or organization, the DOI is associated with.
URI: nmdc:doi_provider
"},{"location":"doi_provider/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_provider/#properties","title":"Properties","text":"name: doi_provider\ndescription: The authority, or organization, the DOI is associated with.\nexamples:\n- value: ess_dive\n description: The corresponding DOI is associated with ESS-DIVE.\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C74932\nrank: 1000\nalias: doi_provider\ndomain_of:\n- Doi\nrange: DoiProviderEnum\n\nA digital object identifier, which is intended to persistantly identify some resource on the web.
URI: nmdc:doi_value
"},{"location":"doi_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Doi A centrally registered identifier symbol used to uniquely identify objects gi... no"},{"location":"doi_value/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
Regex pattern: ^doi:10.\\d{2,9}/.*$
name: doi_value\ndescription: A digital object identifier, which is intended to persistantly identify\n some resource on the web.\nexamples:\n- value: doi:10.46936/10.25585/60000880\n description: The DOI links to an electronic document.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- DOI\n- digital object identifier\nexact_mappings:\n- OBI:0002110\nnarrow_mappings:\n- edam.data:1188\nrank: 1000\nalias: doi_value\ndomain_of:\n- Doi\nrange: uriorcurie\nrequired: true\npattern: ^doi:10.\\d{2,9}/.*$\n\nThe composite type of the door
URI: MIXS:0000795
"},{"location":"door_comp_type/#inheritance","title":"Inheritance","text":"name: door_comp_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The composite type of the door\ntitle: door type, composite\nexamples:\n- value: revolving\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, composite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000795\nalias: door_comp_type\ndomain_of:\n- Biosample\nrange: door_comp_type_enum\nmultivalued: false\n\nThe phsical condition of the door
URI: MIXS:0000788
"},{"location":"door_cond/#inheritance","title":"Inheritance","text":"name: door_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The phsical condition of the door\ntitle: door condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000788\nalias: door_cond\ndomain_of:\n- Biosample\nrange: door_cond_enum\nmultivalued: false\n\nThe direction the door opens
URI: MIXS:0000789
"},{"location":"door_direct/#inheritance","title":"Inheritance","text":"name: door_direct\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The direction the door opens\ntitle: door direction of opening\nexamples:\n- value: inward\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door direction of opening\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000789\nalias: door_direct\ndomain_of:\n- Biosample\nrange: door_direct_enum\nmultivalued: false\n\nThe relative location of the door in the room
URI: MIXS:0000790
"},{"location":"door_loc/#inheritance","title":"Inheritance","text":"name: door_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the door in the room\ntitle: door location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000790\nalias: door_loc\ndomain_of:\n- Biosample\nrange: door_loc_enum\nmultivalued: false\n\nThe material the door is composed of
URI: MIXS:0000791
"},{"location":"door_mat/#inheritance","title":"Inheritance","text":"name: door_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material the door is composed of\ntitle: door material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000791\nalias: door_mat\ndomain_of:\n- Biosample\nrange: door_mat_enum\nmultivalued: false\n\nThe type of movement of the door
URI: MIXS:0000792
"},{"location":"door_move/#inheritance","title":"Inheritance","text":"name: door_move\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of movement of the door\ntitle: door movement\nexamples:\n- value: swinging\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door movement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000792\nalias: door_move\ndomain_of:\n- Biosample\nrange: door_move_enum\nmultivalued: false\n\nThe size of the door
URI: MIXS:0000158
"},{"location":"door_size/#inheritance","title":"Inheritance","text":"name: door_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The size of the door\ntitle: door area or size\nexamples:\n- value: 2.5 square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door area or size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000158\nalias: door_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of door material
URI: MIXS:0000794
"},{"location":"door_type/#inheritance","title":"Inheritance","text":"name: door_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of door material\ntitle: door type\nexamples:\n- value: wooden\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000794\nalias: door_type\ndomain_of:\n- Biosample\nrange: door_type_enum\nmultivalued: false\n\nThe type of metal door
URI: MIXS:0000796
"},{"location":"door_type_metal/#inheritance","title":"Inheritance","text":"name: door_type_metal\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of metal door\ntitle: door type, metal\nexamples:\n- value: hollow\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, metal\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000796\nalias: door_type_metal\ndomain_of:\n- Biosample\nrange: door_type_metal_enum\nmultivalued: false\n\nThe type of wood door
URI: MIXS:0000797
"},{"location":"door_type_wood/#inheritance","title":"Inheritance","text":"name: door_type_wood\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of wood door\ntitle: door type, wood\nexamples:\n- value: battened\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door type, wood\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000797\nalias: door_type_wood\ndomain_of:\n- Biosample\nrange: door_type_wood_enum\nmultivalued: false\n\nSigns of the presence of mold or mildew on a door
URI: MIXS:0000793
"},{"location":"door_water_mold/#inheritance","title":"Inheritance","text":"name: door_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on a door\ntitle: door signs of water/mold\nexamples:\n- value: presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- door signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000793\nalias: door_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nVisible waveband radiance and irradiance measurements in the water column
URI: MIXS:0000703
"},{"location":"down_par/#inheritance","title":"Inheritance","text":"name: down_par\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microEinstein per square meter per second, microEinstein per square centimeter\n per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Visible waveband radiance and irradiance measurements in the water column\ntitle: downward PAR\nexamples:\n- value: 28.71 microEinstein per square meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- downward PAR\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000703\nalias: down_par\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDrainage classification from a standard system such as the USDA system
URI: MIXS:0001085
"},{"location":"drainage_class/#inheritance","title":"Inheritance","text":"name: drainage_class\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Drainage classification from a standard system such as the USDA system\ntitle: drainage classification\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drainage classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001085\nalias: drainage_class\ndomain_of:\n- Biosample\nrange: drainage_class_enum\nmultivalued: false\n\nThe buildings architectural drawings; if design is chosen, indicate phase-conceptual, schematic, design development, and construction documents
URI: MIXS:0000798
"},{"location":"drawings/#inheritance","title":"Inheritance","text":"name: drawings\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The buildings architectural drawings; if design is chosen, indicate phase-conceptual,\n schematic, design development, and construction documents\ntitle: drawings\nexamples:\n- value: sketch\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- drawings\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000798\nalias: drawings\ndomain_of:\n- Biosample\nrange: drawings_enum\nmultivalued: false\n\nThe elapsed time of an activity.
URI: nmdc:duration
"},{"location":"duration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no"},{"location":"duration/#properties","title":"Properties","text":"name: duration\ndescription: The elapsed time of an activity.\nexamples:\n- value: JsonObj(has_numeric_value=2, has_unit='hours')\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: duration\ndomain_of:\n- MixingProcess\n- DissolvingProcess\n- ChemicalConversionProcess\n- MobilePhaseSegment\nrange: QuantityValue\n\nAn ecosystem is a combination of a physical environment (abiotic factors) and all the organisms (biotic factors) that interact with this environment. Ecosystem is in position 1/5 in a GOLD path.
URI: nmdc:ecosystem
"},{"location":"ecosystem/#inheritance","title":"Inheritance","text":"name: ecosystem\ndescription: An ecosystem is a combination of a physical environment (abiotic factors)\n and all the organisms (biotic factors) that interact with this environment. Ecosystem\n is in position 1/5 in a GOLD path.\ncomments:\n- The abiotic factors play a profound role on the type and composition of organisms\n in a given environment. The GOLD Ecosystem at the top of the five-level classification\n system is aimed at capturing the broader environment from which an organism or environmental\n sample is collected. The three broad groups under Ecosystem are Environmental, Host-associated,\n and Engineered. They represent samples collected from a natural environment or from\n another organism or from engineered environments like bioreactors respectively.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nEcosystem categories represent divisions within the ecosystem based on specific characteristics of the environment from where an organism or sample is isolated. Ecosystem category is in position 2/5 in a GOLD path.
URI: nmdc:ecosystem_category
"},{"location":"ecosystem_category/#inheritance","title":"Inheritance","text":"name: ecosystem_category\ndescription: Ecosystem categories represent divisions within the ecosystem based on\n specific characteristics of the environment from where an organism or sample is\n isolated. Ecosystem category is in position 2/5 in a GOLD path.\ncomments:\n- The Environmental ecosystem (for example) is divided into Air, Aquatic and Terrestrial.\n Ecosystem categories for Host-associated samples can be individual hosts or phyla\n and for engineered samples it may be manipulated environments like bioreactors,\n solid waste etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_category\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nA unique id representing the GOLD classifiers associated with a sample.
URI: nmdc:ecosystem_path_id
"},{"location":"ecosystem_path_id/#properties","title":"Properties","text":"name: ecosystem_path_id\ndescription: A unique id representing the GOLD classifiers associated with a sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ecosystem_path_id\nrange: string\n\nEcosystem subtypes represent further subdivision of Ecosystem types into more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.
URI: nmdc:ecosystem_subtype
"},{"location":"ecosystem_subtype/#inheritance","title":"Inheritance","text":"name: ecosystem_subtype\ndescription: Ecosystem subtypes represent further subdivision of Ecosystem types into\n more distinct subtypes. Ecosystem subtype is in position 4/5 in a GOLD path.\ncomments:\n- Ecosystem Type Marine (Environmental -> Aquatic -> Marine) is further divided (for\n example) into Intertidal zone, Coastal, Pelagic, Intertidal zone etc. in the Ecosystem\n subtype category.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_subtype\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nEcosystem types represent things having common characteristics within the Ecosystem Category. These common characteristics based grouping is still broad but specific to the characteristics of a given environment. Ecosystem type is in position 3/5 in a GOLD path.
URI: nmdc:ecosystem_type
"},{"location":"ecosystem_type/#inheritance","title":"Inheritance","text":"name: ecosystem_type\ndescription: Ecosystem types represent things having common characteristics within\n the Ecosystem Category. These common characteristics based grouping is still broad\n but specific to the characteristics of a given environment. Ecosystem type is in\n position 3/5 in a GOLD path.\ncomments:\n- The Aquatic ecosystem category (for example) may have ecosystem types like Marine\n or Thermal springs etc. Ecosystem category Air may have Indoor air or Outdoor air\n as different Ecosystem Types. In the case of Host-associated samples, ecosystem\n type can represent Respiratory system, Digestive system, Roots etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: ecosystem_type\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nPercentage of volatile solids removed from the anaerobic digestor
URI: MIXS:0000657
"},{"location":"efficiency_percent/#inheritance","title":"Inheritance","text":"name: efficiency_percent\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Percentage of volatile solids removed from the anaerobic digestor\ntitle: efficiency percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- efficiency percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000657\nalias: efficiency_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nElevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth's surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit.
URI: MIXS:0000093
"},{"location":"elev/#inheritance","title":"Inheritance","text":"name: elev\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\ndescription: Elevation of the sampling site is its height above a fixed reference\n point, most commonly the mean sea level. Elevation is mainly used when referring\n to points on the earth's surface, while altitude is used for points above the surface,\n such as an aircraft in flight or a spacecraft in orbit.\ntitle: elevation\nexamples:\n- value: 100 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevation\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000093\nalias: elev\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: float\nmultivalued: false\n\nThe number of elevators within the built structure
URI: MIXS:0000799
"},{"location":"elevator/#inheritance","title":"Inheritance","text":"name: elevator\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of elevators within the built structure\ntitle: elevator count\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- elevator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000799\nalias: elevator\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA high-level categorization for how the processed sample is introduced into a mass spectrometer.
URI: nmdc:eluent_introduction_category
"},{"location":"eluent_introduction_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"eluent_introduction_category/#properties","title":"Properties","text":"name: eluent_introduction_category\ndescription: A high-level categorization for how the processed sample is introduced\n into a mass spectrometer.\nexamples:\n- value: liquid_chromatography\n- value: direct_infusion_syringe\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: eluent_introduction_category\ndomain_of:\n- MassSpectrometry\nrange: EluentIntroductionCategoryEnum\n\nAn email address for an entity such as a person. This should be the primary email address used.
URI: schema:email
"},{"location":"email/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"email/#properties","title":"Properties","text":"name: email\ndescription: An email address for an entity such as a person. This should be the primary\n email address used.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: schema:email\nalias: email\ndomain_of:\n- PersonValue\nrange: string\n\nIf true, the data are embargoed and not available for public access.
URI: nmdc:embargoed
"},{"location":"embargoed/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"embargoed/#properties","title":"Properties","text":"Range: Boolean
Recommended: True
name: embargoed\ndescription: If true, the data are embargoed and not available for public access.\ntodos:\n- make this required?\n- first apply to Biosample\n- try to apply to all Biosamples in a particular nmdc-server SubmissionMetadata?\n- applying to a Study may not be granular enough\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: embargoed\ndomain_of:\n- Biosample\nrange: boolean\nrecommended: true\n\nA list of identifiers for the biosample from the EMSL database. This is used to link the biosample, as modeled by NMDC, to the biosample in the planned EMSL NEXUS database.
URI: nmdc:emsl_biosample_identifiers
"},{"location":"emsl_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: emsl_biosample_identifiers\ndescription: A list of identifiers for the biosample from the EMSL database. This\n is used to link the biosample, as modeled by NMDC, to the biosample in the planned\n EMSL NEXUS database.\ntitle: EMSL Biosample Identifiers\ntodos:\n- removed \"planned\" once NEXUS is online\n- determine real expansion for emsl prefix\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- emsl_identifiers\nalias: emsl_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:emsl_identifiers
"},{"location":"emsl_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain emsl_project_identifiers Identifiers that link a NMDC study to the EMSL user facility website hosting ... None Study emsl_biosample_identifiers A list of identifiers for the biosample from the EMSL database None Biosample"},{"location":"emsl_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: emsl_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: emsl_identifiers\nrange: string\n\nIdentifiers that link a NMDC study to the EMSL user facility website hosting the project description of an EMSL user project
URI: nmdc:emsl_project_identifiers
"},{"location":"emsl_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^emsl\\.project:[0-9]{5}$
name: emsl_project_identifiers\ndescription: Identifiers that link a NMDC study to the EMSL user facility website\n hosting the project description of an EMSL user project\ntitle: EMSL Project Identifiers\ntodos:\n- elaborate on description\nnotes:\n- these identifiers are all currently 5 digits long but that could change in the future\nexamples:\n- value: emsl.project:60141\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-schema/issues/927#issuecomment-1802136437\nrank: 1000\nis_a: study_identifiers\nmixins:\n- emsl_identifiers\nalias: emsl_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^emsl\\.project:[0-9]{5}$\n\nThe temperature at which the sample should be stored upon delivery to EMSL
URI: nmdc:emsl_store_temp
"},{"location":"emsl_store_temp/#properties","title":"Properties","text":"Range: String
Recommended: True
name: emsl_store_temp\ndescription: The temperature at which the sample should be stored upon delivery to\n EMSL\ntitle: EMSL sample storage temperature, deg. C\ntodos:\n- add 'see_alsos' with link to NEXUS info\ncomments:\n- Enter a temperature in celsius. Numeric portion only.\nexamples:\n- value: '-80'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{float}'\nalias: emsl_store_temp\nslot_group: EMSL\nrange: string\nrecommended: true\n\nAmount or concentration of substances such as paints, adhesives, mayonnaise, hair colorants, emulsified oils, etc.; can include multiple emulsion types
URI: MIXS:0000660
"},{"location":"emulsions/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: emulsions\nannotations:\n expected_value:\n tag: expected_value\n value: emulsion name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount or concentration of substances such as paints, adhesives, mayonnaise,\n hair colorants, emulsified oils, etc.; can include multiple emulsion types\ntitle: emulsions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- emulsions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000660\nalias: emulsions\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe gene product encoded by this feature. Typically this is used for a CDS feature or gene feature which will encode a protein. It can also be used by a nc transcript ot gene feature that encoded a ncRNA
URI: nmdc:encodes
"},{"location":"encodes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"encodes/#properties","title":"Properties","text":"name: encodes\ndescription: The gene product encoded by this feature. Typically this is used for\n a CDS feature or gene feature which will encode a protein. It can also be used by\n a nc transcript ot gene feature that encoded a ncRNA\ntodos:\n- If we revert Reaction back into the schema, that would be a reasonable domain for\n this slot\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: encodes\ndomain_of:\n- GenomeFeature\nrange: GeneProduct\n\nThe end of the feature in positive 1-based integer coordinates
URI: nmdc:end
"},{"location":"end/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: end\ndescription: The end of the feature in positive 1-based integer coordinates\ncomments:\n- '- \"constraint: end > start\" - \"For features that cross the origin of a circular\n feature, end = the position of the end + the length of the landmark feature.\"'\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:end_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: end\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\nThe date on which any process or activity was ended
URI: nmdc:end_date
"},{"location":"end_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MetabolomicsAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no FiltrationProcess The process of segregation of phases; e no MetatranscriptomeAnnotation no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no CollectingBiosamplesFromSite no MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no LibraryPreparation no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"end_date/#properties","title":"Properties","text":"name: end_date\ndescription: The date on which any process or activity was ended\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: end_date\ndomain_of:\n- PlannedProcess\nrange: string\n\nURI: nmdc:ended_at_time
"},{"location":"ended_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no NomAnalysis no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetaproteomicsAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAssembly no"},{"location":"ended_at_time/#properties","title":"Properties","text":"Range: String
Regex pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$
name: ended_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:endedAtTime\nrank: 1000\nalias: ended_at_time\ndomain_of:\n- WorkflowExecution\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\nReport the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
URI: MIXS:0000012
"},{"location":"env_broad_scale/#inheritance","title":"Inheritance","text":"name: env_broad_scale\nannotations:\n expected_value:\n tag: expected_value\n value: The major environment type(s) where the sample was collected. Recommend\n subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one\n or more pipes.\n tooltip:\n tag: tooltip\n value: The biome or major environmental system where the sample or specimen originated.\n Choose values from subclasses of the 'biome' class [ENVO:00000428] in the Environment\n Ontology (ENVO). For host-associated or plant-associated samples, use terms\n from the UBERON or Plant Ontology to describe the broad anatomical or morphological\n context\ndescription: 'Report the major environmental system the sample or specimen came from.\n The system(s) identified should have a coarse spatial grain, to provide the general\n environmental context of where the sampling was done (e.g. in the desert or a rainforest).\n We recommend using subclasses of EnvO\u2019s biome class: http://purl.obolibrary.org/obo/ENVO_00000428.\n EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'\ntitle: broad-scale environmental context\nexamples:\n- value: oceanic epipelagic zone biome [ENVO:01000035]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- broad-scale environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000012\nalias: env_broad_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nReport the entity or entities which are in the sample or specimen\u2019s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.
URI: MIXS:0000013
"},{"location":"env_local_scale/#inheritance","title":"Inheritance","text":"name: env_local_scale\nannotations:\n expected_value:\n tag: expected_value\n value: Environmental entities having causal influences upon the entity at time\n of sampling.\n tooltip:\n tag: tooltip\n value: The specific environmental entities or features near the sample or specimen\n that significantly influence its characteristics or composition. These entities\n are typically smaller in scale than the broad environmental context. Values\n for this field should be countable, material nouns and must be chosen from subclasses\n of BFO:0000040 (material entity) that appear in the Environment Ontology (ENVO).\n For host-associated or plant-associated samples, use terms from the UBERON or\n Plant Ontology to describe specific anatomical structures or plant parts.\ndescription: 'Report the entity or entities which are in the sample or specimen\u2019s\n local vicinity and which you believe have significant causal influences on your\n sample or specimen. We recommend using EnvO terms which are of smaller spatial grain\n than your entry for env_broad_scale. Terms, such as anatomical sites, from other\n OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in\n this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'\ntitle: local environmental context\nexamples:\n- value: litter layer [ENVO:01000338]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- local environmental context\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000013\nalias: env_local_scale\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nReport the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).
URI: MIXS:0000014
"},{"location":"env_medium/#inheritance","title":"Inheritance","text":"name: env_medium\nannotations:\n expected_value:\n tag: expected_value\n value: The material displaced by the entity at time of sampling. Recommend subclasses\n of environmental material [ENVO:00010483].\n tooltip:\n tag: tooltip\n value: The predominant environmental material or substrate that directly surrounds\n or hosts the sample or specimen at the time of sampling. Choose values from\n subclasses of the 'environmental material' class [ENVO:00010483] in the Environment\n Ontology (ENVO). Values for this field should be measurable or mass material\n nouns, representing continuous environmental materials. For host-associated\n or plant-associated samples, use terms from the UBERON or Plant Ontology to\n indicate a tissue, organ, or plant structure\ndescription: 'Report the environmental material(s) immediately surrounding the sample\n or specimen at the time of sampling. We recommend using subclasses of ''environmental\n material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about\n how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS\n . Terms from other OBO ontologies are permissible as long as they reference mass/volume\n nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree,\n a leaf, a table top).'\ntitle: environmental medium\nexamples:\n- value: soil [ENVO:00001998]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental medium\nrank: 1000\nis_a: environment field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000014\nalias: env_medium\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nMIxS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
URI: nmdc:env_package
"},{"location":"env_package/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"env_package/#properties","title":"Properties","text":"name: env_package\ndescription: MIxS extension for reporting of measurements and observations obtained\n from one or more of the environments where the sample was obtained. All environmental\n packages listed here are further defined in separate subtables. By giving the name\n of the environmental package, a selection of fields can be made from the subtables\n and can be reported\nnotes:\n- no longer in MIxS as of 6.0?\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- environmental package\nrank: 1000\nalias: env_package\ndomain_of:\n- Biosample\nrange: TextValue\n\nfield describing environmental aspect of a sample
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:environment_field
"},{"location":"environment_field/#inheritance","title":"Inheritance","text":"name: environment field\ndescription: field describing environmental aspect of a sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: environment_field\ndomain_of:\n- Biosample\nrange: string\n\nThe number of escalators within the built structure
URI: MIXS:0000800
"},{"location":"escalator/#inheritance","title":"Inheritance","text":"name: escalator\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of escalators within the built structure\ntitle: escalator count\nexamples:\n- value: '4'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- escalator count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000800\nalias: escalator\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of ethylbenzene in the sample
URI: MIXS:0000155
"},{"location":"ethylbenzene/#inheritance","title":"Inheritance","text":"name: ethylbenzene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of ethylbenzene in the sample\ntitle: ethylbenzene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ethylbenzene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000155\nalias: ethylbenzene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nfrom database class
URI: nmdc:etl_software_version
"},{"location":"etl_software_version/#properties","title":"Properties","text":"name: etl_software_version\ndescription: from database class\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: etl_software_version\nrange: string\n\nContains results from evaluating if a Metagenome-Assembled Genome is of eukaryotic lineage.
URI: nmdc:eukaryotic_evaluation
"},{"location":"eukaryotic_evaluation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"eukaryotic_evaluation/#properties","title":"Properties","text":"name: eukaryotic_evaluation\ndescription: Contains results from evaluating if a Metagenome-Assembled Genome is\n of eukaryotic lineage.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: eukaryotic_evaluation\ndomain_of:\n- MagBin\nrange: EukEval\n\nThe computing resource or facility where the workflow was executed.
URI: nmdc:execution_resource
"},{"location":"execution_resource/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no NomAnalysis no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetaproteomicsAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no WorkflowExecution Represents an instance of an execution of a particular workflow yes MetatranscriptomeAssembly no"},{"location":"execution_resource/#properties","title":"Properties","text":"name: execution_resource\ndescription: The computing resource or facility where the workflow was executed.\nexamples:\n- value: NERSC-Cori\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: execution_resource\ndomain_of:\n- WorkflowExecution\nrange: ExecutionResourceEnum\n\nThe amount of exposed ductwork in the room
URI: MIXS:0000144
"},{"location":"exp_duct/#inheritance","title":"Inheritance","text":"name: exp_duct\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The amount of exposed ductwork in the room\ntitle: exposed ductwork\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed ductwork\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000144\nalias: exp_duct\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of exposed pipes in the room
URI: MIXS:0000220
"},{"location":"exp_pipe/#inheritance","title":"Inheritance","text":"name: exp_pipe\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of exposed pipes in the room\ntitle: exposed pipes\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exposed pipes\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000220\nalias: exp_pipe\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nExperimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
URI: MIXS:0000008
"},{"location":"experimental_factor/#inheritance","title":"Inheritance","text":"name: experimental_factor\nannotations:\n expected_value:\n tag: expected_value\n value: text or EFO and/or OBI\ndescription: Experimental factors are essentially the variable aspects of an experiment\n design which can be used to describe an experiment, or set of experiments, in an\n increasingly detailed manner. This field accepts ontology terms from Experimental\n Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a\n browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;\n for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI\ntitle: experimental factor\nexamples:\n- value: time series design [EFO:EFO_0001779]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- experimental factor\nrank: 1000\nis_a: investigation field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000008\nalias: experimental_factor\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nOther details about your sample that you feel can't be accurately represented in the available columns.
URI: nmdc:experimental_factor_other
"},{"location":"experimental_factor_other/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"experimental_factor_other/#properties","title":"Properties","text":"Range: String
Recommended: True
name: experimental_factor_other\ndescription: Other details about your sample that you feel can't be accurately represented\n in the available columns.\ntitle: experimental factor- other\ncomments:\n- This slot accepts open-ended text about your sample.\n- We recommend using key:value pairs.\n- Provided pairs will be considered for inclusion as future slots/terms in this data\n collection template.\nexamples:\n- value: 'experimental treatment: value'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000008\n- MIXS:0000300\nrank: 7\nstring_serialization: '{text}'\nalias: experimental_factor_other\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nThe number of exterior doors in the built structure
URI: MIXS:0000170
"},{"location":"ext_door/#inheritance","title":"Inheritance","text":"name: ext_door\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of exterior doors in the built structure\ntitle: exterior door count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- exterior door count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000170\nalias: ext_door\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe orientation of the exterior wall
URI: MIXS:0000817
"},{"location":"ext_wall_orient/#inheritance","title":"Inheritance","text":"name: ext_wall_orient\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The orientation of the exterior wall\ntitle: orientations of exterior wall\nexamples:\n- value: northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior wall\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000817\nalias: ext_wall_orient\ndomain_of:\n- Biosample\nrange: ext_wall_orient_enum\nmultivalued: false\n\nThe compass direction the exterior window of the room is facing
URI: MIXS:0000818
"},{"location":"ext_window_orient/#inheritance","title":"Inheritance","text":"name: ext_window_orient\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The compass direction the exterior window of the room is facing\ntitle: orientations of exterior window\nexamples:\n- value: southwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- orientations of exterior window\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000818\nalias: ext_window_orient\ndomain_of:\n- Biosample\nrange: ext_window_orient_enum\nmultivalued: false\n\nLink to corresponding identifier in external database
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:external_database_identifiers
"},{"location":"external_database_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: external_database_identifiers\ndescription: Link to corresponding identifier in external database\nnotes:\n- had tried ranges of external identifier and string\ncomments:\n- The value of this field is always a registered CURIE\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- skos:closeMatch\nrank: 1000\nis_a: alternative_identifiers\nabstract: true\nalias: external_database_identifiers\ndomain_of:\n- ProcessedSample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nProvides the target biomolecule that has been separated from a sample during an extraction process.
URI: nmdc:extraction_targets
"},{"location":"extraction_targets/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"extraction_targets/#properties","title":"Properties","text":"Range: ExtractionTargetEnum
Multivalued: True
name: extraction_targets\ndescription: Provides the target biomolecule that has been separated from a sample\n during an extraction process.\nnotes:\n- todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)\nfrom_schema: https://w3id.org/nmdc/nmdc\nnarrow_mappings:\n- NCIT:C177560\n- MIXS:0000037\nrank: 1000\nalias: extraction_targets\ndomain_of:\n- Extraction\nrange: ExtractionTargetEnum\nmultivalued: true\n\nUnusual physical events that may have affected microbial populations
URI: MIXS:0000320
"},{"location":"extreme_event/#inheritance","title":"Inheritance","text":"name: extreme_event\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Unusual physical events that may have affected microbial populations\ntitle: history/extreme events\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/extreme events\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000320\nalias: extreme_event\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nSoil classification from the FAO World Reference Database for Soil Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups
URI: MIXS:0001083
"},{"location":"fao_class/#inheritance","title":"Inheritance","text":"name: fao_class\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Soil classification from the FAO World Reference Database for Soil Resources.\n The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups\ntitle: soil_taxonomic/FAO classification\nexamples:\n- value: Luvisols\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/FAO classification\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001083\nalias: fao_class\ndomain_of:\n- Biosample\nrange: fao_class_enum\nmultivalued: false\n\nA Sequence Ontology term that describes the category of a feature
URI: nmdc:feature_category
"},{"location":"feature_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e no GenomeFeature A feature localized to an interval along a genome no"},{"location":"feature_category/#properties","title":"Properties","text":"name: feature_category\ndescription: A Sequence Ontology term that describes the category of a feature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_category\ndomain_of:\n- GenomeFeature\n- FunctionalAnnotation\nrange: ControlledIdentifiedTermValue\n\nTODO: Yuri to write
URI: nmdc:feature_type
"},{"location":"feature_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"feature_type/#properties","title":"Properties","text":"name: feature_type\ndescription: 'TODO: Yuri to write'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: feature_type\ndomain_of:\n- GenomeFeature\nrange: string\n\nInformation about treatment involving the use of fertilizers; should include the name of fertilizer, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fertilizer regimens
URI: MIXS:0000556
"},{"location":"fertilizer_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: fertilizer_regm\nannotations:\n expected_value:\n tag: expected_value\n value: fertilizer name;fertilizer amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the use of fertilizers; should\n include the name of fertilizer, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple fertilizer regimens\ntitle: fertilizer regimen\nexamples:\n- value: urea;0.6 milligram per liter;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fertilizer regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000556\nalias: fertilizer_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nName of the hydrocarbon field (e.g. Albacora)
URI: MIXS:0000291
"},{"location":"field/#inheritance","title":"Inheritance","text":"name: field\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the hydrocarbon field (e.g. Albacora)\ntitle: field name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- field name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000291\nalias: field\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:field_research_site_set
"},{"location":"field_research_site_set/#inheritance","title":"Inheritance","text":"Range: FieldResearchSite
Multivalued: True
name: field_research_site_set\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: field_research_site_set\ndomain_of:\n- Database\nrange: FieldResearchSite\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nSize of the file in bytes
URI: nmdc:file_size_bytes
"},{"location":"file_size_bytes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"file_size_bytes/#properties","title":"Properties","text":"name: file_size_bytes\ndescription: Size of the file in bytes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: file_size_bytes\ndomain_of:\n- DataObject\nrange: bytes\n\nA porous material on which solid particles present in air or other fluid which flows through it are largely caught and retained.
URI: nmdc:filter_material
"},{"location":"filter_material/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filter_material/#properties","title":"Properties","text":"name: filter_material\ndescription: A porous material on which solid particles present in air or other fluid\n which flows through it are largely caught and retained.\ncomments:\n- 'Filters are made with a variety of materials: cellulose and derivatives, glass\n fibre, ceramic, synthetic plastics and fibres. Filters may be naturally porous or\n be made so by mechanical or other means. Membrane/ceramic filters are prepared with\n highly controlled pore size in a sheet of suitable material such as polyfluoroethylene,\n polycarbonate or cellulose esters. Nylon mesh is sometimes used for reinforcement.\n The pores constitute 80\u201385% of the filter volume commonly and several pore sizes\n are available for air sampling (0.45\u22120.8 \u03bcm are commonly employed).'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filter_material\ndomain_of:\n- FiltrationProcess\nrange: string\n\nType of filter used or how the sample was filtered
URI: nmdc:filter_method
"},{"location":"filter_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"filter_method/#properties","title":"Properties","text":"Range: String
Recommended: True
name: filter_method\ndescription: Type of filter used or how the sample was filtered\ntitle: filter method\ncomments:\n- describe the filter or provide a catalog number and manufacturer\nexamples:\n- value: C18\n- value: Basix PES, 13-100-106 FisherSci\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000765\nrank: 6\nstring_serialization: '{text}'\nalias: filter_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nA quantitative or qualitative measurement of the physical dimensions of the pores in a material.
URI: nmdc:filter_pore_size
"},{"location":"filter_pore_size/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filter_pore_size/#properties","title":"Properties","text":"name: filter_pore_size\ndescription: A quantitative or qualitative measurement of the physical dimensions\n of the pores in a material.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filter_pore_size\ndomain_of:\n- FiltrationProcess\nrange: QuantityValue\n\nA device which removes solid particulates or airborne molecular contaminants
URI: MIXS:0000765
"},{"location":"filter_type/#inheritance","title":"Inheritance","text":"Range: FilterTypeEnum
Multivalued: True
name: filter_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: A device which removes solid particulates or airborne molecular contaminants\ntitle: filter type\nexamples:\n- value: HEPA\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- filter type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000765\nalias: filter_type\ndomain_of:\n- Biosample\nrange: filter_type_enum\nmultivalued: true\n\nThe type of conditioning applied to a filter, device, etc.
URI: nmdc:filtration_category
"},{"location":"filtration_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"filtration_category/#properties","title":"Properties","text":"name: filtration_category\ndescription: The type of conditioning applied to a filter, device, etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: filtration_category\ndomain_of:\n- FiltrationProcess\nrange: string\n\nWhen solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in the combination
URI: nmdc:final_concentration
"},{"location":"final_concentration/#inheritance","title":"Inheritance","text":"name: final_concentration\ndescription: When solutions A (containing substance X) and B are combined together,\n this slot captures the concentration of X in the combination\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: concentration\nalias: final_concentration\ndomain_of:\n- PortionOfSubstance\nrange: QuantityValue\n\nHistorical and/or physical evidence of fire
URI: MIXS:0001086
"},{"location":"fire/#inheritance","title":"Inheritance","text":"name: fire\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Historical and/or physical evidence of fire\ntitle: history/fire\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/fire\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001086\nalias: fire\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nA firebox with chimney
URI: MIXS:0000802
"},{"location":"fireplace_type/#inheritance","title":"Inheritance","text":"name: fireplace_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A firebox with chimney\ntitle: fireplace type\nexamples:\n- value: wood burning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fireplace type\nrank: 1000\nis_a: core field\nstring_serialization: '[gas burning|wood burning]'\nslot_uri: MIXS:0000802\nalias: fireplace_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nHistorical and/or physical evidence of flooding
URI: MIXS:0000319
"},{"location":"flooding/#inheritance","title":"Inheritance","text":"name: flooding\nannotations:\n expected_value:\n tag: expected_value\n value: date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Historical and/or physical evidence of flooding\ntitle: history/flooding\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/flooding\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000319\nalias: flooding\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe time period since installment of the carpet or flooring
URI: MIXS:0000164
"},{"location":"floor_age/#inheritance","title":"Inheritance","text":"name: floor_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: years, weeks, days\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The time period since installment of the carpet or flooring\ntitle: floor age\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000164\nalias: floor_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe area of the floor space within the room
URI: MIXS:0000165
"},{"location":"floor_area/#inheritance","title":"Inheritance","text":"name: floor_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The area of the floor space within the room\ntitle: floor area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000165\nalias: floor_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000803
"},{"location":"floor_cond/#inheritance","title":"Inheritance","text":"name: floor_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the floor at the time of sampling; photos or\n video preferred; use drawings to indicate location of damaged areas\ntitle: floor condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000803\nalias: floor_cond\ndomain_of:\n- Biosample\nrange: floor_cond_enum\nmultivalued: false\n\nThe number of floors in the building, including basements and mechanical penthouse
URI: MIXS:0000225
"},{"location":"floor_count/#inheritance","title":"Inheritance","text":"name: floor_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of floors in the building, including basements and mechanical\n penthouse\ntitle: floor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000225\nalias: floor_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe floor covering type; the finished surface that is walked on
URI: MIXS:0000804
"},{"location":"floor_finish_mat/#inheritance","title":"Inheritance","text":"name: floor_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The floor covering type; the finished surface that is walked on\ntitle: floor finish material\nexamples:\n- value: carpet\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000804\nalias: floor_finish_mat\ndomain_of:\n- Biosample\nrange: floor_finish_mat_enum\nmultivalued: false\n\nRefers to the structural elements and subfloor upon which the finish flooring is installed
URI: MIXS:0000806
"},{"location":"floor_struc/#inheritance","title":"Inheritance","text":"name: floor_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the structural elements and subfloor upon which the finish\n flooring is installed\ntitle: floor structure\nexamples:\n- value: concrete\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000806\nalias: floor_struc\ndomain_of:\n- Biosample\nrange: floor_struc_enum\nmultivalued: false\n\nThe ability of the floor to provide inertia against temperature fluctuations
URI: MIXS:0000166
"},{"location":"floor_thermal_mass/#inheritance","title":"Inheritance","text":"name: floor_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the floor to provide inertia against temperature fluctuations\ntitle: floor thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000166\nalias: floor_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSigns of the presence of mold or mildew in a room
URI: MIXS:0000805
"},{"location":"floor_water_mold/#inheritance","title":"Inheritance","text":"name: floor_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew in a room\ntitle: floor signs of water/mold\nexamples:\n- value: ceiling discoloration\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- floor signs of water/mold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000805\nalias: floor_water_mold\ndomain_of:\n- Biosample\nrange: floor_water_mold_enum\nmultivalued: false\n\nRaw or converted fluorescence of water
URI: MIXS:0000704
"},{"location":"fluor/#inheritance","title":"Inheritance","text":"name: fluor\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram chlorophyll a per cubic meter, volts\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Raw or converted fluorescence of water\ntitle: fluorescence\nexamples:\n- value: 2.5 volts\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fluorescence\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000704\nalias: fluor\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of times the sample location is cleaned. Frequency of cleaning might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.
URI: MIXS:0000226
"},{"location":"freq_clean/#inheritance","title":"Inheritance","text":"name: freq_clean\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration or {text}\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times the sample location is cleaned. Frequency of cleaning\n might be on a Daily basis, Weekly, Monthly, Quarterly or Annually.\ntitle: frequency of cleaning\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cleaning\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000226\nalias: freq_clean\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of times a meal is cooked per week
URI: MIXS:0000227
"},{"location":"freq_cook/#inheritance","title":"Inheritance","text":"name: freq_cook\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times a meal is cooked per week\ntitle: frequency of cooking\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- frequency of cooking\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000227\nalias: freq_cook\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:functional_annotation_agg
"},{"location":"functional_annotation_agg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Database An abstract holder for any set of metadata and data no"},{"location":"functional_annotation_agg/#properties","title":"Properties","text":"Range: FunctionalAnnotationAggMember
Multivalued: True
name: functional_annotation_agg\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: functional_annotation_agg\ndomain_of:\n- Database\nrange: FunctionalAnnotationAggMember\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of all functional annotations
URI: nmdc:functional_annotation_set
"},{"location":"functional_annotation_set/#inheritance","title":"Inheritance","text":"Range: FunctionalAnnotation
Multivalued: True
name: functional_annotation_set\ndescription: This property links a database object to the set of all functional annotations\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: functional_annotation_set\ndomain_of:\n- Database\nrange: FunctionalAnnotation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA list of organizations, along with the award numbers, that underwrite financial support for projects of a particular type. Typically, they process applications and award funds to the chosen qualified applicants.
URI: nmdc:funding_sources
"},{"location":"funding_sources/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"funding_sources/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: funding_sources\ndescription: A list of organizations, along with the award numbers, that underwrite\n financial support for projects of a particular type. Typically, they process applications\n and award funds to the chosen qualified applicants.\ncomments:\n- Include only the name of the funding organization and the award or contract number.\nexamples:\n- value: National Sciences Foundation Dimensions of Biodiversity (award no. 1342701)\n- value: U.S. Department of Energy, Office of Science, Office of Biological and Environmental\n Research (BER) under contract DE-AC05-00OR2275\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- NCIT:C39409\nrank: 1000\nalias: funding_sources\ndomain_of:\n- Study\nrange: string\nmultivalued: true\n\nInformation about treatment involving use of fungicides; should include the name of fungicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple fungicide regimens
URI: MIXS:0000557
"},{"location":"fungicide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: fungicide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: fungicide name;fungicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of fungicides; should include\n the name of fungicide, amount administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple fungicide regimens\ntitle: fungicide regimen\nexamples:\n- value: bifonazole;1 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- fungicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000557\nalias: fungicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe types of furniture present in the sampled room
URI: MIXS:0000807
"},{"location":"furniture/#inheritance","title":"Inheritance","text":"name: furniture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The types of furniture present in the sampled room\ntitle: furniture\nexamples:\n- value: chair\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- furniture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000807\nalias: furniture\ndomain_of:\n- Biosample\nrange: furniture_enum\nmultivalued: false\n\nThe gap size percentage of all scaffolds.
URI: nmdc:gap_pct
"},{"location":"gap_pct/#inheritance","title":"Inheritance","text":"name: gap_pct\ndescription: The gap size percentage of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gap_pct\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nUse of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens
URI: MIXS:0000558
"},{"location":"gaseous_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gaseous_environment\nannotations:\n expected_value:\n tag: expected_value\n value: gaseous compound name;gaseous compound amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Use of conditions with differing gaseous environments; should include\n the name of gaseous compound, amount administered, treatment duration, interval\n and total experimental duration; can include multiple gaseous environment regimens\ntitle: gaseous environment\nexamples:\n- value: nitric oxide;0.5 micromole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000558\nalias: gaseous_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAmount or concentration of substances such as hydrogen sulfide, carbon dioxide, methane, etc.; can include multiple substances
URI: MIXS:0000661
"},{"location":"gaseous_substances/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gaseous_substances\nannotations:\n expected_value:\n tag: expected_value\n value: gaseous substance name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Amount or concentration of substances such as hydrogen sulfide, carbon\n dioxide, methane, etc.; can include multiple substances\ntitle: gaseous substances\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gaseous substances\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000661\nalias: gaseous_substances\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAverage of GC content of all contigs.
URI: nmdc:gc_avg
"},{"location":"gc_avg/#inheritance","title":"Inheritance","text":"name: gc_avg\ndescription: Average of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_avg\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nStandard deviation of GC content of all contigs.
URI: nmdc:gc_std
"},{"location":"gc_std/#inheritance","title":"Inheritance","text":"name: gc_std\ndescription: Standard deviation of GC content of all contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: gc_std\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe gender type of the restroom
URI: MIXS:0000808
"},{"location":"gender_restroom/#inheritance","title":"Inheritance","text":"name: gender_restroom\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The gender type of the restroom\ntitle: gender of restroom\nexamples:\n- value: male\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gender of restroom\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000808\nalias: gender_restroom\ndomain_of:\n- Biosample\nrange: gender_restroom_enum\nmultivalued: false\n\nNumber of genes.
URI: nmdc:gene_count
"},{"location":"gene_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gene_count/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: gene_count\ndescription: Number of genes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_count\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nThe identifier for the gene function.
URI: nmdc:gene_function_id
"},{"location":"gene_function_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotationAggMember no"},{"location":"gene_function_id/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
name: gene_function_id\ndescription: The identifier for the gene function.\nexamples:\n- value: KEGG.ORTHOLOGY:K00627\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gene_function_id\ndomain_of:\n- FunctionalAnnotationAggMember\nrange: uriorcurie\nrequired: true\n\ncalibration information is generated a process
URI: nmdc:generates_calibration
"},{"location":"generates_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"generates_calibration/#properties","title":"Properties","text":"name: generates_calibration\ndescription: calibration information is generated a process\ncomments:\n- A gas chromatography mass spectromery run generates data to calibrate the retention\n index\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: generates_calibration\ndomain_of:\n- MassSpectrometry\nrange: CalibrationInformation\nstructured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n\nGenetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection
URI: MIXS:0000859
"},{"location":"genetic_mod/#inheritance","title":"Inheritance","text":"name: genetic_mod\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Genetic modifications of the genome of an organism, which may occur naturally\n by spontaneous mutation, or be introduced by some experimental means, e.g. specification\n of a transgene or the gene knocked-out or details of transient transfection\ntitle: genetic modification\nexamples:\n- value: aox1A transgenic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- genetic modification\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000859\nalias: genetic_mod\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThis property links a database object to the set of all features
URI: nmdc:genome_feature_set
"},{"location":"genome_feature_set/#inheritance","title":"Inheritance","text":"Range: GenomeFeature
Multivalued: True
name: genome_feature_set\ndescription: This property links a database object to the set of all features\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: genome_feature_set\ndomain_of:\n- Database\nrange: GenomeFeature\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)
URI: MIXS:0000010
"},{"location":"geo_loc_name/#inheritance","title":"Inheritance","text":"name: geo_loc_name\nannotations:\n expected_value:\n tag: expected_value\n value: 'country or sea name (INSDC or GAZ): region(GAZ), specific location name'\ndescription: The geographical origin of the sample as defined by the country or sea\n name followed by specific region name. Country or sea names should be chosen from\n the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (http://purl.bioontology.org/ontology/GAZ)\ntitle: geographic location (country and/or sea,region)\nexamples:\n- value: 'USA: Maryland, Bethesda'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (country and/or sea,region)\nrank: 1000\nis_a: environment field\nstring_serialization: '{term}: {term}, {text}'\nslot_uri: MIXS:0000010\nalias: geo_loc_name\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA positive 1-based integer coordinate indicating start or end
URI: nmdc:gff_coordinate
"},{"location":"gff_coordinate/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: gff_coordinate\ndescription: A positive 1-based integer coordinate indicating start or end\ncomments:\n- For features that cross the origin of a circular feature (e.g. most bacterial genomes,\n plasmids, and some viral genomes), the requirement for start to be less than or\n equal to end is satisfied by making end = the position of the end + the length of\n the landmark feature.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: gff_coordinate\nrange: integer\nminimum_value: 1\n\nThe url that points to the exact github location of a workflow.
URI: nmdc:git_url
"},{"location":"git_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no NomAnalysis no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetaproteomicsAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no WorkflowExecution Represents an instance of an execution of a particular workflow yes MetatranscriptomeAssembly no"},{"location":"git_url/#properties","title":"Properties","text":"name: git_url\ndescription: The url that points to the exact github location of a workflow.\nexamples:\n- value: https://github.com/microbiomedata/mg_annotation/releases/tag/0.1\n- value: https://github.com/microbiomedata/metaMS/blob/master/metaMS/gcmsWorkflow.py\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: git_url\ndomain_of:\n- WorkflowExecution\nrange: string\n\nMeasurement of glucosidase activity
URI: MIXS:0000137
"},{"location":"glucosidase_act/#inheritance","title":"Inheritance","text":"name: glucosidase_act\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mol per liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of glucosidase activity\ntitle: glucosidase activity\nexamples:\n- value: 5 mol per liter per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- glucosidase activity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000137\nalias: glucosidase_act\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:gnps_identifiers
"},{"location":"gnps_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gnps_task_identifiers identifiers that link a NMDC study to a web-based report about metabolomics a... None Study"},{"location":"gnps_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: gnps_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: gnps_identifiers\nrange: string\n\nidentifiers that link a NMDC study to a web-based report about metabolomics analysis progress and results
URI: nmdc:gnps_task_identifiers
"},{"location":"gnps_task_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gnps\\.task:[a-f0-9]+$
name: gnps_task_identifiers\ndescription: identifiers that link a NMDC study to a web-based report about metabolomics\n analysis progress and results\ntitle: GNPS task identifiers\ncomments:\n- this could be considered a related identifier, as the metabolomics progress and\n results aren't a study per se\n- this identifier was registered with bioregistry but not identifiers.org\nexamples:\n- value: gnps.task:4b848c342a4f4abc871bdf8a09a60807\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://microbiomedata.github.io/nmdc-schema/MetabolomicsAnalysis/\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gnps_identifiers\nalias: gnps_task_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^gnps\\.task:[a-f0-9]+$\n\nidentifiers for corresponding analysis projects in GOLD
URI: nmdc:gold_analysis_project_identifiers
"},{"location":"gold_analysis_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Ga[0-9]+$
name: gold_analysis_project_identifiers\ndescription: identifiers for corresponding analysis projects in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Ga0526289\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- gold_identifiers\nalias: gold_analysis_project_identifiers\ndomain_of:\n- MetagenomeAnnotation\n- MetatranscriptomeAnnotation\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Ga[0-9]+$\n\nidentifiers for corresponding sample in GOLD
URI: nmdc:gold_biosample_identifiers
"},{"location":"gold_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: Uriorcurie
Multivalued: True
Regex pattern: ^gold:Gb[0-9]+$
name: gold_biosample_identifiers\ndescription: identifiers for corresponding sample in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gb0312930\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- gold_identifiers\nalias: gold_biosample_identifiers\ndomain_of:\n- Biosample\nrange: uriorcurie\nmultivalued: true\npattern: ^gold:Gb[0-9]+$\n\nURI: nmdc:gold_identifiers
"},{"location":"gold_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain gold_study_identifiers identifiers for corresponding project(s) in GOLD None Study gold_biosample_identifiers identifiers for corresponding sample in GOLD uriorcurie Biosample gold_sequencing_project_identifiers identifiers for corresponding sequencing project in GOLD None NucleotideSequencing gold_analysis_project_identifiers identifiers for corresponding analysis projects in GOLD None MetatranscriptomeAnnotation, MetagenomeAnnotation"},{"location":"gold_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: gold_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: gold_identifiers\nrange: string\n\nThis is a grouping for any of the gold path fields
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:gold_path_field
"},{"location":"gold_path_field/#inheritance","title":"Inheritance","text":"name: gold_path_field\nannotations:\n tooltip:\n tag: tooltip\n value: GOLD Ecosystem Classification paths describe the surroundings from which\n an environmental sample or an organism is collected.\n annotations:\n source:\n tag: source\n value: https://gold.jgi.doe.gov/ecosystem_classification\ndescription: This is a grouping for any of the gold path fields\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: gold_path_field\nrange: string\n\nidentifiers for corresponding sequencing project in GOLD
URI: nmdc:gold_sequencing_project_identifiers
"},{"location":"gold_sequencing_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gp[0-9]+$
name: gold_sequencing_project_identifiers\ndescription: identifiers for corresponding sequencing project in GOLD\nexamples:\n- value: https://bioregistry.io/gold:Gp0108335\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: omics_processing_identifiers\nmixins:\n- gold_identifiers\nalias: gold_sequencing_project_identifiers\ndomain_of:\n- NucleotideSequencing\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Gp[0-9]+$\n\nidentifiers for corresponding project(s) in GOLD
URI: nmdc:gold_study_identifiers
"},{"location":"gold_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^gold:Gs[0-9]+$
name: gold_study_identifiers\ndescription: identifiers for corresponding project(s) in GOLD\ntitle: GOLD Study Identifiers\ncomments:\n- uses the prefix GS (but possibly in a different case)\nexamples:\n- value: https://bioregistry.io/gold:Gs0110115\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/studies\nrank: 1000\nis_a: study_identifiers\nmixins:\n- gold_identifiers\nalias: gold_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^gold:Gs[0-9]+$\n\nWhether or not subject is gravid, and if yes date due or date post-conception, specifying which is used
URI: MIXS:0000875
"},{"location":"gravidity/#inheritance","title":"Inheritance","text":"name: gravidity\nannotations:\n expected_value:\n tag: expected_value\n value: gravidity status;timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Whether or not subject is gravid, and if yes date due or date post-conception,\n specifying which is used\ntitle: gravidity\nexamples:\n- value: yes;due date:2018-05-11\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravidity\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{timestamp}'\nslot_uri: MIXS:0000875\nalias: gravidity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about treatment involving use of gravity factor to study various types of responses in presence, absence or modified levels of gravity; treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple treatments
URI: MIXS:0000559
"},{"location":"gravity/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: gravity\nannotations:\n expected_value:\n tag: expected_value\n value: gravity factor value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: meter per square second, g\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of gravity factor to study\n various types of responses in presence, absence or modified levels of gravity; treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n treatments\ntitle: gravity\nexamples:\n- value: 12 g;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- gravity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000559\nalias: gravity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nType of facility where the sampled plant was grown; controlled vocabulary: growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research
URI: MIXS:0001043
"},{"location":"growth_facil/#inheritance","title":"Inheritance","text":"name: growth_facil\nannotations:\n expected_value:\n tag: expected_value\n value: free text or CO\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Type of facility where the sampled plant was grown; controlled vocabulary:\n growth chamber, open top chamber, glasshouse, experimental garden, field. Alternatively\n use Crop Ontology (CO) terms, see http://www.cropontology.org/ontology/CO_715/Crop%20Research'\ntitle: growth facility\nexamples:\n- value: Growth chamber [CO_715:0000189]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth facility\nrank: 1000\nis_a: core field\nstring_serialization: '{text}|{termLabel} {[termID]}'\nslot_uri: MIXS:0001043\nalias: growth_facil\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nCharacteristic shape, appearance or growth form of a plant species
URI: MIXS:0001044
"},{"location":"growth_habit/#inheritance","title":"Inheritance","text":"name: growth_habit\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Characteristic shape, appearance or growth form of a plant species\ntitle: growth habit\nexamples:\n- value: spreading\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth habit\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001044\nalias: growth_habit\ndomain_of:\n- Biosample\nrange: growth_habit_enum\nmultivalued: false\n\nInformation about treatment involving use of growth hormones; should include the name of growth hormone, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple growth hormone regimens
URI: MIXS:0000560
"},{"location":"growth_hormone_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: growth_hormone_regm\nannotations:\n expected_value:\n tag: expected_value\n value: growth hormone name;growth hormone amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of growth hormones; should\n include the name of growth hormone, amount administered, treatment regimen including\n how many times the treatment was repeated, how long each treatment lasted, and the\n start and end time of the entire treatment; can include multiple growth hormone\n regimens\ntitle: growth hormone regimen\nexamples:\n- value: abscisic acid;0.5 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- growth hormone regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000560\nalias: growth_hormone_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTaxonomic class assigned by GTDB-Tk.
URI: nmdc:gtdbtk_class
"},{"location":"gtdbtk_class/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_class/#properties","title":"Properties","text":"name: gtdbtk_class\ndescription: Taxonomic class assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:class\nrank: 1000\nalias: gtdbtk_class\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic domain assigned by GTDB-Tk.
URI: nmdc:gtdbtk_domain
"},{"location":"gtdbtk_domain/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_domain/#properties","title":"Properties","text":"name: gtdbtk_domain\ndescription: Taxonomic domain assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:superkingdom\nrank: 1000\nalias: gtdbtk_domain\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic family assigned by GTDB-Tk.
URI: nmdc:gtdbtk_family
"},{"location":"gtdbtk_family/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_family/#properties","title":"Properties","text":"name: gtdbtk_family\ndescription: Taxonomic family assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:family\nrank: 1000\nalias: gtdbtk_family\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic genus assigned by GTDB-Tk.
URI: nmdc:gtdbtk_genus
"},{"location":"gtdbtk_genus/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_genus/#properties","title":"Properties","text":"name: gtdbtk_genus\ndescription: Taxonomic genus assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:genus\nrank: 1000\nalias: gtdbtk_genus\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic order assigned by GTDB-Tk.
URI: nmdc:gtdbtk_order
"},{"location":"gtdbtk_order/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_order/#properties","title":"Properties","text":"name: gtdbtk_order\ndescription: Taxonomic order assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:order\nrank: 1000\nalias: gtdbtk_order\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic phylum assigned by GTDB-Tk.
URI: nmdc:gtdbtk_phylum
"},{"location":"gtdbtk_phylum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_phylum/#properties","title":"Properties","text":"name: gtdbtk_phylum\ndescription: Taxonomic phylum assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:phylum\nrank: 1000\nalias: gtdbtk_phylum\ndomain_of:\n- MagBin\nrange: string\n\nTaxonomic genus assigned by GTDB-Tk.
URI: nmdc:gtdbtk_species
"},{"location":"gtdbtk_species/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"gtdbtk_species/#properties","title":"Properties","text":"name: gtdbtk_species\ndescription: Taxonomic genus assigned by GTDB-Tk.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://doi.org/10.1093/bioinformatics/btz848\nexact_mappings:\n- NCBITaxon:species\nrank: 1000\nalias: gtdbtk_species\ndomain_of:\n- MagBin\nrange: string\n\nURI: nmdc:habitat
"},{"location":"habitat/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no Biosample Biological source material which can be characterized by an experiment no"},{"location":"habitat/#properties","title":"Properties","text":"name: habitat\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: habitat\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: string\n\nThe total count of hallways and cooridors in the built structure
URI: MIXS:0000228
"},{"location":"hall_count/#inheritance","title":"Inheritance","text":"name: hall_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total count of hallways and cooridors in the built structure\ntitle: hallway/corridor count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hallway/corridor count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000228\nalias: hall_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe handidness of the individual sampled
URI: MIXS:0000809
"},{"location":"handidness/#inheritance","title":"Inheritance","text":"name: handidness\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The handidness of the individual sampled\ntitle: handidness\nexamples:\n- value: right handedness\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- handidness\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000809\nalias: handidness\ndomain_of:\n- Biosample\nrange: handidness_enum\nmultivalued: false\n\nLinks a quantity value to a boolean
URI: nmdc:has_boolean_value
"},{"location":"has_boolean_value/#properties","title":"Properties","text":"name: has_boolean_value\ndescription: Links a quantity value to a boolean\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_boolean_value\nrange: boolean\n\nThe identifier of the associated ChromatographyConfiguration, providing information about how a sample was introduced into the mass spectrometer.
URI: nmdc:has_chromatography_configuration
"},{"location":"has_chromatography_configuration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"has_chromatography_configuration/#properties","title":"Properties","text":"name: has_chromatography_configuration\ndescription: The identifier of the associated ChromatographyConfiguration, providing\n information about how a sample was introduced into the mass spectrometer.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_chromatography_configuration\ndomain_of:\n- MassSpectrometry\nrange: ChromatographyConfiguration\n\nThis slot links a study to a credit association. The credit association will be linked to a person value and to a CRediT Contributor Roles term. Overall semantics: person should get credit X for their participation in the study
URI: prov:qualifiedAssociation
"},{"location":"has_credit_associations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"has_credit_associations/#properties","title":"Properties","text":"Range: CreditAssociation
Multivalued: True
name: has_credit_associations\nannotations:\n tooltip:\n tag: tooltip\n value: Other researchers associated with this study.\ndescription: 'This slot links a study to a credit association. The credit association\n will be linked to a person value and to a CRediT Contributor Roles term. Overall\n semantics: person should get credit X for their participation in the study'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nslot_uri: prov:qualifiedAssociation\nalias: has_credit_associations\ndomain_of:\n- Study\nrange: CreditAssociation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:has_failure_categorization
"},{"location":"has_failure_categorization/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MetabolomicsAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no FiltrationProcess The process of segregation of phases; e no MetatranscriptomeAnnotation no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no CollectingBiosamplesFromSite no MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no LibraryPreparation no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"has_failure_categorization/#properties","title":"Properties","text":"Range: FailureCategorization
Multivalued: True
name: has_failure_categorization\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_failure_categorization\ndomain_of:\n- PlannedProcess\nrange: FailureCategorization\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:has_function
"},{"location":"has_function/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FunctionalAnnotation An assignment of a function term (e yes"},{"location":"has_function/#properties","title":"Properties","text":"Range: String
Regex pattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$
name: has_function\nnotes:\n- the range for has_function was asserted as functional_annotation_term/FunctionalAnnotationTerm,\n- but is actually taking string arguments in MongoDB,\n- and those are frequently fulltext, not CURIEs. MAM 2021-06-23\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_function\ndomain_of:\n- FunctionalAnnotation\nrange: string\npattern: ^(KEGG_PATHWAY:\\w{2,4}\\d{5}|KEGG.REACTION:R\\d+|RHEA:\\d{5}|MetaCyc:[A-Za-z0-9+_.%-:]+|EC:\\d{1,2}(\\.\\d{0,3}){0,3}|GO:\\d{7}|MetaNetX:(MNXR\\d+|EMPTY)|SEED:\\w+|KEGG\\.ORTHOLOGY:K\\d+|EGGNOG:\\w+|PFAM:PF\\d{5}|TIGRFAM:TIGR\\d+|SUPFAM:\\w+|CATH:[1-6]\\.[0-9]+\\.[0-9]+\\.[0-9]+|PANTHER.FAMILY:PTHR\\d{5}(\\:SF\\d{1,3})?)$\n\nAn input to a process.
URI: nmdc:has_input
"},{"location":"has_input/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes MetabolomicsAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... yes MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... yes FiltrationProcess The process of segregation of phases; e yes MetatranscriptomeAnnotation yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material yes CollectingBiosamplesFromSite yes MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts yes ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no LibraryPreparation yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... yes WorkflowExecution Represents an instance of an execution of a particular workflow yes"},{"location":"has_input/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: has_input\ndescription: An input to a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- input\nrank: 1000\nalias: has_input\ndomain_of:\n- PlannedProcess\nrange: NamedThing\nmultivalued: true\n\nThe identifier of the associated MassSpectrometryConfiguration.
URI: nmdc:has_mass_spectrometry_configuration
"},{"location":"has_mass_spectrometry_configuration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes"},{"location":"has_mass_spectrometry_configuration/#properties","title":"Properties","text":"name: has_mass_spectrometry_configuration\ndescription: The identifier of the associated MassSpectrometryConfiguration.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_mass_spectrometry_configuration\ndomain_of:\n- MassSpectrometry\nrange: MassSpectrometryConfiguration\n\nThe maximum value part, expressed as number, of the quantity value when the value covers a range.
URI: nmdc:has_maximum_numeric_value
"},{"location":"has_maximum_numeric_value/#inheritance","title":"Inheritance","text":"name: has_maximum_numeric_value\ndescription: The maximum value part, expressed as number, of the quantity value when\n the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_maximum_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\nURI: nmdc:has_metabolite_identifications
"},{"location":"has_metabolite_identifications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysis no"},{"location":"has_metabolite_identifications/#properties","title":"Properties","text":"Range: MetaboliteIdentification
Multivalued: True
name: has_metabolite_identifications\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_metabolite_identifications\ndomain_of:\n- MetabolomicsAnalysis\nrange: MetaboliteIdentification\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe minimum value part, expressed as number, of the quantity value when the value covers a range.
URI: nmdc:has_minimum_numeric_value
"},{"location":"has_minimum_numeric_value/#inheritance","title":"Inheritance","text":"name: has_minimum_numeric_value\ndescription: The minimum value part, expressed as number, of the quantity value when\n the value covers a range.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: has_numeric_value\nalias: has_minimum_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\nLinks a quantity value to a number
URI: nmdc:has_numeric_value
"},{"location":"has_numeric_value/#inheritance","title":"Inheritance","text":"name: has_numeric_value\ndescription: Links a quantity value to a number\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- qud:quantityValue\n- schema:value\nrank: 1000\nalias: has_numeric_value\ndomain_of:\n- QuantityValue\nrange: decimal\n\nAn output from a process.
URI: nmdc:has_output
"},{"location":"has_output/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes MetabolomicsAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... yes MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... yes FiltrationProcess The process of segregation of phases; e yes MetatranscriptomeAnnotation yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material yes CollectingBiosamplesFromSite yes MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts yes ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no LibraryPreparation yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... yes WorkflowExecution Represents an instance of an execution of a particular workflow yes"},{"location":"has_output/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: has_output\ndescription: An output from a process.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- output\nrank: 1000\nalias: has_output\ndomain_of:\n- PlannedProcess\nrange: NamedThing\nmultivalued: true\n\nURI: nmdc:has_peptide_quantifications
","text":""},{"location":"has_peptide_quantifications/#properties","title":"Properties","text":"Range: PeptideQuantification
Multivalued: True
name: has_peptide_quantifications\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_peptide_quantifications\nrange: PeptideQuantification\nmultivalued: true\ninlined_as_list: true\n\nA list of process parts that make up a protocol.
URI: nmdc:has_process_parts
"},{"location":"has_process_parts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProtocolExecution A PlannedProces that has PlannedProcess parts yes"},{"location":"has_process_parts/#properties","title":"Properties","text":"Range: PlannedProcess
Multivalued: True
Required: True
name: has_process_parts\ndescription: A list of process parts that make up a protocol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: has_process_parts\ndomain_of:\n- ProtocolExecution\nrange: PlannedProcess\nrequired: true\nmultivalued: true\n\nThe value that was specified for an annotation in raw form, i.e. a string. E.g. \"2 cm\" or \"2-4 cm\"
URI: nmdc:has_raw_value
"},{"location":"has_raw_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TimestampValue A value that is a timestamp no AttributeValue The value for any value of a attribute for a sample no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no GeolocationValue A normalized value for a location on the earth's surface yes TextValue A basic string value no QuantityValue A simple quantity, e yes PersonValue An attribute value representing a person yes ControlledTermValue A controlled term or class from an ontology no ImageValue An attribute value representing an image no"},{"location":"has_raw_value/#properties","title":"Properties","text":"name: has_raw_value\ndescription: The value that was specified for an annotation in raw form, i.e. a string.\n E.g. \"2 cm\" or \"2-4 cm\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: has_raw_value\ndomain_of:\n- AttributeValue\nrange: string\n\nLinks a QuantityValue to a unit
URI: nmdc:has_unit
"},{"location":"has_unit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot QuantityValue A simple quantity, e yes"},{"location":"has_unit/#properties","title":"Properties","text":"name: has_unit\ndescription: Links a QuantityValue to a unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- scale\nmappings:\n- qud:unit\n- schema:unitCode\nrank: 1000\nalias: has_unit\ndomain_of:\n- QuantityValue\nrange: unit\n\nMain hydrocarbon type produced from resource (i.e. Oil, gas, condensate, etc). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000989
"},{"location":"hc_produced/#inheritance","title":"Inheritance","text":"name: hc_produced\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main hydrocarbon type produced from resource (i.e. Oil, gas, condensate,\n etc). If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: hydrocarbon type produced\nexamples:\n- value: Gas\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon type produced\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000989\nalias: hc_produced\ndomain_of:\n- Biosample\nrange: hc_produced_enum\nmultivalued: false\n\nMain Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined as a natural environmental feature containing large amounts of hydrocarbons at high concentrations potentially suitable for commercial exploitation. This term should not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich environments with currently limited commercial interest such as seeps, outcrops, gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000988
"},{"location":"hcr/#inheritance","title":"Inheritance","text":"name: hcr\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Main Hydrocarbon Resource type. The term \"Hydrocarbon Resource\" HCR defined\n as a natural environmental feature containing large amounts of hydrocarbons at high\n concentrations potentially suitable for commercial exploitation. This term should\n not be confused with the Hydrocarbon Occurrence term which also includes hydrocarbon-rich\n environments with currently limited commercial interest such as seeps, outcrops,\n gas hydrates etc. If \"other\" is specified, please propose entry in \"additional info\"\n field\ntitle: hydrocarbon resource type\nexamples:\n- value: Oil Sand\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000988\nalias: hcr\ndomain_of:\n- Biosample\nrange: hcr_enum\nmultivalued: false\n\nOriginal formation water salinity (prior to secondary recovery e.g. Waterflooding) expressed as TDS
URI: MIXS:0000406
"},{"location":"hcr_fw_salinity/#inheritance","title":"Inheritance","text":"name: hcr_fw_salinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original formation water salinity (prior to secondary recovery e.g. Waterflooding)\n expressed as TDS\ntitle: formation water salinity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- formation water salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000406\nalias: hcr_fw_salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nGeological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000993
"},{"location":"hcr_geol_age/#inheritance","title":"Inheritance","text":"name: hcr_geol_age\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Geological age of hydrocarbon resource (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: hydrocarbon resource geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000993\nalias: hcr_geol_age\ndomain_of:\n- Biosample\nrange: hcr_geol_age_enum\nmultivalued: false\n\nOriginal pressure of the hydrocarbon resource
URI: MIXS:0000395
"},{"location":"hcr_pressure/#inheritance","title":"Inheritance","text":"name: hcr_pressure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: atmosphere, kilopascal\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original pressure of the hydrocarbon resource\ntitle: hydrocarbon resource original pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original pressure\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000395\nalias: hcr_pressure\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nOriginal temperature of the hydrocarbon resource
URI: MIXS:0000393
"},{"location":"hcr_temp/#inheritance","title":"Inheritance","text":"name: hcr_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original temperature of the hydrocarbon resource\ntitle: hydrocarbon resource original temperature\nexamples:\n- value: 150-295 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- hydrocarbon resource original temperature\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000393\nalias: hcr_temp\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMethods of conditioning or heating a room or building
URI: MIXS:0000766
"},{"location":"heat_cool_type/#inheritance","title":"Inheritance","text":"Range: HeatCoolTypeEnum
Multivalued: True
name: heat_cool_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Methods of conditioning or heating a room or building\ntitle: heating and cooling system type\nexamples:\n- value: heat pump\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating and cooling system type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000766\nalias: heat_cool_type\ndomain_of:\n- Biosample\nrange: heat_cool_type_enum\nmultivalued: true\n\nThe location of heat delivery within the room
URI: MIXS:0000810
"},{"location":"heat_deliv_loc/#inheritance","title":"Inheritance","text":"name: heat_deliv_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The location of heat delivery within the room\ntitle: heating delivery locations\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating delivery locations\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000810\nalias: heat_deliv_loc\ndomain_of:\n- Biosample\nrange: heat_deliv_loc_enum\nmultivalued: false\n\nThe method by which the heat is delivered through the system
URI: MIXS:0000812
"},{"location":"heat_sys_deliv_meth/#inheritance","title":"Inheritance","text":"name: heat_sys_deliv_meth\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The method by which the heat is delivered through the system\ntitle: heating system delivery method\nexamples:\n- value: radiant\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system delivery method\nrank: 1000\nis_a: core field\nstring_serialization: '[conductive|radiant]'\nslot_uri: MIXS:0000812\nalias: heat_sys_deliv_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe heating system identifier
URI: MIXS:0000833
"},{"location":"heat_system_id/#inheritance","title":"Inheritance","text":"name: heat_system_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The heating system identifier\ntitle: heating system identifier\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- heating system identifier\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000833\nalias: heat_system_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nHeavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field.
URI: MIXS:0000652
"},{"location":"heavy_metals/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: heavy_metals\nannotations:\n expected_value:\n tag: expected_value\n value: heavy metal name;measurement value unit\n preferred_unit:\n tag: preferred_unit\n value: microgram per gram\n occurrence:\n tag: occurrence\n value: m\ndescription: Heavy metals present in the sequenced sample and their concentrations.\n For multiple heavy metals and concentrations, add multiple copies of this field.\ntitle: extreme_unusual_properties/heavy metals\nexamples:\n- value: mercury;0.09 micrograms per gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000652\nalias: heavy_metals\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nReference or method used in determining heavy metals
URI: MIXS:0000343
"},{"location":"heavy_metals_meth/#inheritance","title":"Inheritance","text":"name: heavy_metals_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining heavy metals\ntitle: extreme_unusual_properties/heavy metals method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- extreme_unusual_properties/heavy metals method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000343\nalias: heavy_metals_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\ninlined: true\ninlined_as_list: true\n\nThe average carpet fiber height in the indoor environment
URI: MIXS:0000167
"},{"location":"height_carper_fiber/#inheritance","title":"Inheritance","text":"name: height_carper_fiber\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average carpet fiber height in the indoor environment\ntitle: height carpet fiber mat\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- height carpet fiber mat\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000167\nalias: height_carper_fiber\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving use of herbicides; information about treatment involving use of growth hormones; should include the name of herbicide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000561
"},{"location":"herbicide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: herbicide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: herbicide name;herbicide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of herbicides; information\n about treatment involving use of growth hormones; should include the name of herbicide,\n amount administered, treatment regimen including how many times the treatment was\n repeated, how long each treatment lasted, and the start and end time of the entire\n treatment; can include multiple regimens\ntitle: herbicide regimen\nexamples:\n- value: atrazine;10 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- herbicide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000561\nalias: herbicide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:highest_similarity_score
"},{"location":"highest_similarity_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"highest_similarity_score/#properties","title":"Properties","text":"name: highest_similarity_score\ntodos:\n- Yuri to fill in description\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: highest_similarity_score\ndomain_of:\n- MetaboliteIdentification\nrange: float\n\nThe website address (URL) of an entity's homepage.
URI: nmdc:homepage_website
"},{"location":"homepage_website/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
Regex pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$
name: homepage_website\ndescription: The website address (URL) of an entity's homepage.\nexamples:\n- value: https://www.neonscience.org/\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: websites\nalias: homepage_website\ndomain_of:\n- Study\nrange: string\nmultivalued: true\npattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\nmaximum_cardinality: 1\n\nReference or method used in determining the horizon
URI: MIXS:0000321
"},{"location":"horizon_meth/#inheritance","title":"Inheritance","text":"name: horizon_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the horizon\ntitle: soil horizon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000321\nalias: horizon_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nAge of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees
URI: MIXS:0000255
"},{"location":"host_age/#inheritance","title":"Inheritance","text":"name: host_age\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: year, day, hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Age of host at the time of sampling; relevant scale depends on species\n and study, e.g. Could be seconds for amoebae or centuries for trees\ntitle: host age\nexamples:\n- value: 10 days\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000255\nalias: host_age\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nOriginal body habitat where the sample was obtained from
URI: MIXS:0000866
"},{"location":"host_body_habitat/#inheritance","title":"Inheritance","text":"name: host_body_habitat\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original body habitat where the sample was obtained from\ntitle: host body habitat\nexamples:\n- value: nasopharynx\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body habitat\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000866\nalias: host_body_habitat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSubstance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon
URI: MIXS:0000888
"},{"location":"host_body_product/#inheritance","title":"Inheritance","text":"name: host_body_product\nannotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Substance produced by the body, e.g. Stool, mucus, where the sample was\n obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy\n ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or\n https://www.ebi.ac.uk/ols/ontologies/uberon\ntitle: host body product\nexamples:\n- value: mucus [UBERON:0000912]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body product\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000888\nalias: host_body_product\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nName of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
URI: MIXS:0000867
"},{"location":"host_body_site/#inheritance","title":"Inheritance","text":"name: host_body_site\nannotations:\n expected_value:\n tag: expected_value\n value: FMA or UBERON\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of body site where the sample was obtained from, such as a specific\n organ or tissue (tongue, lung etc...). For foundational model of anatomy ontology\n (fma) (v 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms,\n please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON\ntitle: host body site\nexamples:\n- value: gill [UBERON:0002535]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body site\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000867\nalias: host_body_site\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nCore body temperature of the host when sample was collected
URI: MIXS:0000274
"},{"location":"host_body_temp/#inheritance","title":"Inheritance","text":"name: host_body_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Core body temperature of the host when sample was collected\ntitle: host body temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host body temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000274\nalias: host_body_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe color of host
URI: MIXS:0000260
"},{"location":"host_color/#inheritance","title":"Inheritance","text":"name: host_color\nannotations:\n expected_value:\n tag: expected_value\n value: color\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The color of host\ntitle: host color\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host color\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000260\nalias: host_color\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nCommon name of the host.
URI: MIXS:0000248
"},{"location":"host_common_name/#inheritance","title":"Inheritance","text":"name: host_common_name\nannotations:\n expected_value:\n tag: expected_value\n value: common name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Common name of the host.\ntitle: host common name\nexamples:\n- value: human\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host common name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000248\nalias: host_common_name\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nType of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
URI: MIXS:0000869
"},{"location":"host_diet/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: host_diet\nannotations:\n expected_value:\n tag: expected_value\n value: diet type\n occurrence:\n tag: occurrence\n value: m\ndescription: Type of diet depending on the host, for animals omnivore, herbivore etc.,\n for humans high-fat, meditteranean etc.; can include multiple diet types\ntitle: host diet\nexamples:\n- value: herbivore\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host diet\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000869\nalias: host_diet\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nList of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text
URI: MIXS:0000031
"},{"location":"host_disease_stat/#inheritance","title":"Inheritance","text":"name: host_disease_stat\nannotations:\n expected_value:\n tag: expected_value\n value: disease name or Disease Ontology term\ndescription: List of diseases with which the host has been diagnosed; can include\n multiple diagnoses. The value of the field depends on host; for humans the terms\n should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,\n non-human host diseases are free text\ntitle: host disease status\nexamples:\n- value: rabies [DOID:11260]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host disease status\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000031\nalias: host_disease_stat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMeasurement of dry mass
URI: MIXS:0000257
"},{"location":"host_dry_mass/#inheritance","title":"Inheritance","text":"name: host_dry_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of dry mass\ntitle: host dry mass\nexamples:\n- value: 500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host dry mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000257\nalias: host_dry_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nFamilial relationships to other hosts in the same study; can include multiple relationships
URI: MIXS:0000872
"},{"location":"host_family_relation/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_family_relation\nannotations:\n expected_value:\n tag: expected_value\n value: relationship type;arbitrary identifier\n occurrence:\n tag: occurrence\n value: m\ndescription: Familial relationships to other hosts in the same study; can include\n multiple relationships\ntitle: host family relationship\nexamples:\n- value: offspring;Mussel25\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host family relationship\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0000872\nalias: host_family_relation\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\nObserved genotype
URI: MIXS:0000365
"},{"location":"host_genotype/#inheritance","title":"Inheritance","text":"name: host_genotype\nannotations:\n expected_value:\n tag: expected_value\n value: genotype\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Observed genotype\ntitle: host genotype\nexamples:\n- value: C57BL/6\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host genotype\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000365\nalias: host_genotype\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nLiterature reference giving growth conditions of the host
URI: MIXS:0000871
"},{"location":"host_growth_cond/#inheritance","title":"Inheritance","text":"name: host_growth_cond\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Literature reference giving growth conditions of the host\ntitle: host growth conditions\nexamples:\n- value: https://academic.oup.com/icesjms/article/68/2/349/617247\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host growth conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0000871\nalias: host_growth_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe height of subject
URI: MIXS:0000264
"},{"location":"host_height/#inheritance","title":"Inheritance","text":"name: host_height\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The height of subject\ntitle: host height\nexamples:\n- value: 0.1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000264\nalias: host_height\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nContent of last meal and time since feeding; can include multiple values
URI: MIXS:0000870
"},{"location":"host_last_meal/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: host_last_meal\nannotations:\n expected_value:\n tag: expected_value\n value: content;duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Content of last meal and time since feeding; can include multiple values\ntitle: host last meal\nexamples:\n- value: corn feed;P2H\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host last meal\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000870\nalias: host_last_meal\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe length of subject
URI: MIXS:0000256
"},{"location":"host_length/#inheritance","title":"Inheritance","text":"name: host_length\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: centimeter, millimeter, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The length of subject\ntitle: host length\nexamples:\n- value: 1 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host length\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000256\nalias: host_length\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDescription of life stage of host
URI: MIXS:0000251
"},{"location":"host_life_stage/#inheritance","title":"Inheritance","text":"name: host_life_stage\nannotations:\n expected_value:\n tag: expected_value\n value: stage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of life stage of host\ntitle: host life stage\nexamples:\n- value: adult\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host life stage\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000251\nalias: host_life_stage\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:host_name
"},{"location":"host_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"host_name/#properties","title":"Properties","text":"name: host_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: host_name\ndomain_of:\n- Biosample\nrange: string\n\nPhenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
URI: MIXS:0000874
"},{"location":"host_phenotype/#inheritance","title":"Inheritance","text":"name: host_phenotype\nannotations:\n expected_value:\n tag: expected_value\n value: PATO or HP\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Phenotype of human or other host. For phenotypic quality ontology (pato)\n (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For\n Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP\ntitle: host phenotype\nexamples:\n- value: elongated [PATO:0001154]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host phenotype\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000874\nalias: host_phenotype\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nGender or physical sex of the host.
URI: MIXS:0000811
"},{"location":"host_sex/#inheritance","title":"Inheritance","text":"name: host_sex\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Gender or physical sex of the host.\ntitle: host sex\nexamples:\n- value: non-binary\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000811\nalias: host_sex\ndomain_of:\n- Biosample\nrange: host_sex_enum\nmultivalued: false\n\nMorphological shape of host
URI: MIXS:0000261
"},{"location":"host_shape/#inheritance","title":"Inheritance","text":"name: host_shape\nannotations:\n expected_value:\n tag: expected_value\n value: shape\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Morphological shape of host\ntitle: host shape\nexamples:\n- value: round\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host shape\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000261\nalias: host_shape\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA unique identifier by which each subject can be referred to, de-identified.
URI: MIXS:0000861
"},{"location":"host_subject_id/#inheritance","title":"Inheritance","text":"name: host_subject_id\nannotations:\n expected_value:\n tag: expected_value\n value: unique identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A unique identifier by which each subject can be referred to, de-identified.\ntitle: host subject id\nexamples:\n- value: MPI123\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subject id\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000861\nalias: host_subject_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.
URI: MIXS:0001318
"},{"location":"host_subspecf_genlin/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_subspecf_genlin\nannotations:\n expected_value:\n tag: expected_value\n value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,\n e.g. serovar, biotype, ecotype, variety, cultivar.\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about the genetic distinctness of the host organism below\n the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,\n or any relevant genetic typing schemes like Group I plasmid. Subspecies should not\n be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name\n and the lineage rank separated by a colon, e.g., biovar:abc123.\ntitle: host subspecific genetic lineage\nexamples:\n- value: 'serovar:Newport, variety:glabrum, cultivar: Red Delicious'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host subspecific genetic lineage\nrank: 1000\nis_a: core field\nstring_serialization: '{rank name}:{text}'\nslot_uri: MIXS:0001318\nalias: host_subspecf_genlin\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\nThe growth substrate of the host.
URI: MIXS:0000252
"},{"location":"host_substrate/#inheritance","title":"Inheritance","text":"name: host_substrate\nannotations:\n expected_value:\n tag: expected_value\n value: substrate name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The growth substrate of the host.\ntitle: host substrate\nexamples:\n- value: rock\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host substrate\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000252\nalias: host_substrate\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.
URI: MIXS:0001298
"},{"location":"host_symbiont/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: host_symbiont\nannotations:\n expected_value:\n tag: expected_value\n value: species name or common name\n occurrence:\n tag: occurrence\n value: m\ndescription: The taxonomic name of the organism(s) found living in mutualistic, commensalistic,\n or parasitic symbiosis with the specific host.\ntitle: observed host symbionts\nexamples:\n- value: flukeworms\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- observed host symbionts\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001298\nalias: host_symbiont\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\nNCBI taxon id of the host, e.g. 9606
URI: MIXS:0000250
"},{"location":"host_taxid/#inheritance","title":"Inheritance","text":"name: host_taxid\nannotations:\n expected_value:\n tag: expected_value\n value: NCBI taxon identifier\n occurrence:\n tag: occurrence\n value: '1'\ndescription: NCBI taxon id of the host, e.g. 9606\ntitle: host taxid\ncomments:\n- Homo sapiens [NCBITaxon:9606] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host taxid\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000250\nalias: host_taxid\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nTotal mass of the host at collection, the unit depends on host
URI: MIXS:0000263
"},{"location":"host_tot_mass/#inheritance","title":"Inheritance","text":"name: host_tot_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total mass of the host at collection, the unit depends on host\ntitle: host total mass\nexamples:\n- value: 2500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host total mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000263\nalias: host_tot_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of wet mass
URI: MIXS:0000567
"},{"location":"host_wet_mass/#inheritance","title":"Inheritance","text":"name: host_wet_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilogram, gram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of wet mass\ntitle: host wet mass\nexamples:\n- value: 1500 gram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- host wet mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000567\nalias: host_wet_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nAmount of water vapour in the air, at the time of sampling
URI: MIXS:0000100
"},{"location":"humidity/#inheritance","title":"Inheritance","text":"name: humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Amount of water vapour in the air, at the time of sampling\ntitle: humidity\nexamples:\n- value: 25 gram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000100\nalias: humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving an exposure to varying degree of humidity; information about treatment involving use of growth hormones; should include amount of humidity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000568
"},{"location":"humidity_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: humidity_regm\nannotations:\n expected_value:\n tag: expected_value\n value: humidity value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to varying degree of\n humidity; information about treatment involving use of growth hormones; should include\n amount of humidity administered, treatment regimen including how many times the\n treatment was repeated, how long each treatment lasted, and the start and end time\n of the entire treatment; can include multiple regimens\ntitle: humidity regimen\nexamples:\n- value: 25 gram per cubic meter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- humidity regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000568\nalias: humidity_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
URI: nmdc:id
"},{"location":"id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes MetabolomicsAnalysis yes Study A study summarizes the overall goal of a research initiative and outlines the... yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... yes NomAnalysis yes DissolvingProcess A mixing step where a soluble component is mixed with a liquid component yes Site no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... yes GeneProduct A molecule encoded by a gene that has an evolved function no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes CalibrationInformation A calibration object that is associated with a process yes FiltrationProcess The process of segregation of phases; e yes MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ProcessedSample yes MetatranscriptomeAnnotation yes Biosample Biological source material which can be characterized by an experiment yes MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... yes MetagenomeSequencing Initial sequencing activity that precedes any analysis yes NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated yes Pooling physical combination of several instances of like material yes CollectingBiosamplesFromSite yes MetaproteomicsAnalysis yes MixingProcess The combining of components, particles or layers into a more homogeneous stat... yes EnvironmentalMaterialTerm no MetatranscriptomeAssembly yes Extraction A material separation in which a desired component of an input material is se... yes Sample A sample is a material entity that can be characterized by an experiment no ChemicalEntity An atom or molecule that can be represented with a chemical formula no MaterialEntity no Instrument A material entity that is designed to perform a function in a scientific inve... yes NamedThing a databased entity or concept/class no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes Manifest A qualified collection of DataObjects that can be analyzed together in the sa... yes OrthologyGroup A set of genes or gene products in which all members are orthologous no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... yes OntologyClass A representation of class defined in an external ontology yes Configuration A set of parameters that define the actions of a process and is shared among ... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... yes ProtocolExecution A PlannedProces that has PlannedProcess parts yes ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no LibraryPreparation yes ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes DataObject An object that primarily consists of symbols that represent information yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"id/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: id\ndescription: A unique identifier for a thing. Must be either a CURIE shorthand for\n a URI or a complete URI\nnotes:\n- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'\n- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters\n will be accepted\n- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked\n via per-class id slot usage assertions\n- minting authority shoulders should probably be enumerated and checked in the pattern\nexamples:\n- value: nmdc:mgmag-00-x012.1_7_c1\n description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248\nfrom_schema: https://w3id.org/nmdc/nmdc\nstructured_aliases:\n workflow_execution_id:\n literal_form: workflow_execution_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\n data_object_id:\n literal_form: data_object_id\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- NamedThing\nrange: uriorcurie\nrequired: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nIdentifiers are crucial for the NMDC, both for any data objects created (aka minted) and for any external objects that are being referenced in NMDC.
Examples of entities that require identifiers:
Identifiers should be:
See McMurry et al, PMID:28662064 for more desiderata.
"},{"location":"identifiers/#curies-prefixed-ids","title":"CURIEs - prefixed IDs","text":"Following McMurry et al. we adopt the use of prefixed identifiers
The syntax is:
Prefix:LocalId\nExamples:
These prefixed identifiers are also known as CURIEs (Compact URIs). There is a W3C specification for these.
All prefixes should be registered with at least one standard identifier prefix system. If a prefix is not already registered, please open a ticket at Bioregistry.io to request registration. If an entity is registered in multiple registries (possibly with differing syntax or case), we recommend using the bioregistry.io registry as the primary source of truth.
Popular choices for identifier registry services include:
BIOSAMPLE:SAMEA2397676)","text":"Description Registry Entry Resolvable Link Bioregistry.io https://bioregistry.io/registry/biosample https://bioregistry.io/biosample:SAMEA2397676 Identifiers.org https://registry.identifiers.org/registry/biosample https://identifiers.org/BIOSAMPLE:SAMEA2397676 N2T.net http://n2t.net/BIOSAMPLE:SAMEA2397676"},{"location":"identifiers/#2-gold-identifiers-example-curie-goldgp0119849","title":"2. GOLD identifiers (Example CURIE: GOLD:Gp0119849)","text":"Description Registry Entry Resolvable Link Bioregistry.io https://bioregistry.io/registry/gold https://bioregistry.io/gold:Gp0119849 Identifiers.org https://registry.identifiers.org/registry/gold https://identifiers.org/GOLD:Gp0119849 N2T.net N/A http://n2t.net/GOLD:Gp0119849"},{"location":"identifiers/#identifiers-for-ontology-terms-and-function-descriptors","title":"identifiers for ontology terms and function descriptors","text":"Most of the ontologies we use are in OBO. All OBO IDs are prefixed using the ontology ID space. The list of ID spaces can be found on: http://obofoundry.org, and use a special resolver service called \"PURL\" (Permanent URL) to resolve the ID to a URL.
For example the ID/CURIE ENVO:00002007 represents the class sediment and is expanded to a URI of http://purl.obolibrary.org/obo/ENVO_00002007
KEGG is actually a set of databases, each with its own prefix, usually of form KEGG.$database, e.g.
The NMDC Schema is annotated with the set of IDs, ordered by preference, that are allowed to act as primary keys for instances of each class. For example the class OrthologyGroup has a description of the IDs allowed on the class web page, the first listed is KEGG.ORTHOLOGY. The full URL for each is in the jsonld context file, jsonschema/nmdc.context.jsonld.
The underlying yaml looks like this:
orthology group:\n is_a: functional annotation term\n description: >-\n A set of genes or gene products in which all members are orthologous\n id_prefixes:\n - KEGG.ORTHOLOGY ## KO number\n - EGGNOG\n - PFAM\n - TIGRFAM\n - SUPFAM\n - PANTHER.FAMILY\n exact_mappings:\n - biolink:GeneFamily\nThe NMDC Schema specifies legal identifiers for all of its classes. All data instances/records that are intended for upload into the NMDC metadata store must have an id field that follows this specification. Ids that are minted at NMDC must match this abstract pattern:
nmdc:<type-code>-<shoulder>-<blade><.version><_locus>\nThe abstract pattern has six parts, delimited by hyphens (unless otherwise specified):
nmdc: All NMDC identifiers will begin with this static prefix.
<typecode>: An alphabetical code with a 1:1 correspondence to a class from the NMDC Schema. Answers the question \"of what class is the data record that bears this id\"? Must consist of 1 to 6 lower case letters, although a minimum of 3 letters is suggested. The type code portion of an NMDC id must match the regular expression [a-z]{1,6}.
<shoulder>: A code that indicates what organization minted the identifier. Shoulder values must be zero to six lower case letters, flanked by one digit on either side. Answers the question \"what organization minted this id\"? The central identifier endpoint, hosted at LBL, uses the shoulder 00. Should organizations like JGI or EMSL need to mint identifiers in bulk, they would be assigned other shoulders, so that id values aren't reused. The shoulder portion of an NMDC id must match the regular expression [0-9][a-z]{0,6}[0-9].
<blade>: The fully unique part of the identifier under a given type code and shoulder namespace. The shoulder and blade together make up the key of the identifier. The blade is an alphanumeric string of open-ended length with at least one character, following the regular expression: [A-Za-z0-9]+.
<.version>: Differentiates multiple iterations of a workflow. The delimiter used to separate the version from the blade and everything before it is a dot (.). The version is a potentially repeating alphanumeric pattern with a minimum length of 1 character. The version portion of an NMDC id must match the regular expression (\\.[A-Za-z0-9]+)*.
<_locus>: Indicates the contig on which a genomic feature is found, along with its start and end coordinates. Delimited from the rest of the id by an underscore (_). The locus part, if present, must have at least one character from the set off uppercase letters, lower case letters, digits, underscores (_), dots (.) and hyphens (-). The regular expression that the locus will follow is: _[A-Za-z0-9_\\.-]+.
The per-part regular expression described above can be composed into one complete regular expression. Named capture groups have been used to tie in the part names.
^(?<prefix>nmdc):(?<typecode>[a-z]{1,6})-(?<shoulder>[0-9][a-z]{0,6}[0-9])-(?<blade>[A-Za-z0-9]+)(?<version>(\\.[A-Za-z0-9]+)*)(?<locus>_[A-Za-z0-9_\\.-]+)?$\nNMDC offers a central identifier minting endpoint in order to save data contributors the trouble of hand-crafting ids. The possibility of decentralized (or offline) minting of ids by trusted organizations has also been anticipated. id component 3 below (the shoulder) is used to indicate the organization that minted an id. LBL, which hosts the id minting endpoint will use one shoulder value. If another organization, like JGI or EMSL, needs to bulk-create ids outside of the central identifier minting endpoint, they would use different shoulders, to be determined by the NMDC Schema and metadata team.
Both metaG and metaT analyses produce GFF3 files. See issue 184 for more on how the GFF is modeled.
The main entity identifier used in NMDC is the gene product ID. This identifier is used in functioanl annotations. This is typically a protein encoded by a CDS, e.g.
Ga0185794_41 GeneMark.hmm-2 v1.05 CDS 48 1037 56.13 + 0 ID=Ga0185794_41_48_1037;translation_table=11;start_type=ATG;product=5-methylthioadenosine/S-adenosylhomocysteine deaminase;product_source=KO:K12960;cath_funfam=3.20.20.140;cog=COG0402;ko=KO:K12960;ec_number=EC:3.5.4.28,EC:3.5.4.31;pfam=PF01979;superfamily=51338,51556\nNote: when processing GFF column 9 values, NMDC first ensures that each ID in this field is correctly prefixed according to the NMDC Schema id_prefixes directives. In the example above, KO:K12960 is translated to KEGG.OTHOLOGY:K12960 to make sure the data is compliant with the registered prefix authorities and thus the NMDC Schema. This helps to ensure that the data is interoperable and can be used in a variety of tools and services beyond NMDC.
In 2023 NMDC transitioned from reusing identifiers from other organizations to using NMDC minted identifiers as the primary identifier.
"},{"location":"identifiers/#identifier-mapping","title":"Identifier mapping","text":"Identifier Example NMDC Schema Class NMDC Schema Slot gold:Gs* gold:Gs0114675 Study gold_study_identifiers gold:Gb* gold:Gb0110739 Biosample gold_biosample_identifiers emsl:* emsl:63ca2f94-6647-11eb-ae93-0242ac130002 Biosample emsl_biosample_identifiers igsn:* igsn:IEWFS001H Biosample igsn_biosample_identifiers gold:Gp* gold:Gp0452734 OmicsProcessing gold_sequencing_project_identifiers emsl:* emsl:598506 OmicsProcessing alternative_identifiersSome legacy data object identifiers were based on file md5sums, either with or without a prefix (nmdc, jgi, emsl). In some cases the legacy value can be found by removing the prefix and searching DataObject records on slot md5_checksum. If you are having trouble finding information based on legacy identifiers please contact support@microbiomedata.org.
"},{"location":"identifiers/#additional-details-on-legacy-identifiers","title":"Additional details on legacy identifiers","text":"Legacy metagenomics objects look like this:
id: \"gold:Gp0108335\"\n name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n has_input:\n - \"gold:Gb0108335\"\n part_of:\n - \"gold:Gs0112340\"\n has_output:\n - \"jgi:551a20d30d878525404e90d5\"\n omics_type: Metagenome\n type: \"nmdc:OmicsProcessing\"\n add_date: \"30-OCT-14 12.00.00.000000000 AM\"\n mod_date: \"22-MAY-20 06.13.12.927000000 PM\"\n ncbi_project_name: \"Thawing permafrost microbial communities from the Arctic, studying carbon transformations - Permafrost 712P3D\"\n processing_institution: \"Joint Genome Institute\"\n principal_investigator_name: \"Virginia Rich\"\nthe linked data object uses a jgi prefix and an md5 hash
id: \"jgi:551a20d30d878525404e90d5\"\n name: \"8871.1.114459.GCCAAT.fastq.gz\"\n description: \"Raw sequencer read data\"\n file_size_bytes: 17586370657\n type: \"nmdc:DataObject\"\nLegacy metaproteomics objects look like this:
id: \"emsl:404590\"\n name: \"FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n description: \"High res MS with low res CID MSn\"\n part_of:\n - \"gold:Gs0110132\"\n has_output:\n - \"emsl:output_404590\"\n omics_type: Proteomics\n type: \"nmdc:OmicsProcessing\"\n instrument_name: \"VOrbiETD03\"\n processing_institution: \"Environmental Molecular Sciences Lab\"\nand the output data objects are formed from these:
id: \"emsl:output_404590\"\n name: \"output: FECB_21_5093B_01_23Dec14_Tiger_14-11-12\"\n description: \"High res MS with low res CID MSn\"\n file_size_bytes: 503296678\n type: \"nmdc:DataObject\"\nthe data objects use hashes (md5) prefixed with nmdc:
name: \"404590_resultant.tsv\"\n description: \"Aggregation of analysis tools{MSGFplus, MASIC} results\"\n file_size_bytes: 10948480\n type: \"nmdc:DataObject\"\n id: \"nmdc:e0c70280a7a23c7c5cc1e589f72e896e\"\nWe are working with the GSC to provide permanent IDs for MIxS terms. Note these terms are schema-level rather than data-level. For now we place these in the NMDC namespaces, e.g nmdc:alt
Using LinkML's default tooling, we produce a JSON-LD context with the schema:
When this is combined with schema-conformant JSON, RDF can be automatically created using the intended URIs
Please see: Maintaining identifiers] for more information on developing and maintaining identifiers in the schema.
"},{"location":"igsn_biosample_identifiers/","title":"Slot: IGSN Biosample Identifiers (igsn_biosample_identifiers)","text":"A list of identifiers for the biosample from the IGSN database.
URI: nmdc:igsn_biosample_identifiers
"},{"location":"igsn_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: igsn_biosample_identifiers\ndescription: A list of identifiers for the biosample from the IGSN database.\ntitle: IGSN Biosample Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- igsn_identifiers\nalias: igsn_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:igsn_identifiers
"},{"location":"igsn_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain igsn_biosample_identifiers A list of identifiers for the biosample from the IGSN database None Biosample"},{"location":"igsn_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: igsn_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: igsn_identifiers\nrange: string\n\nA list of identifiers that relate the biosample to records in the IMG database.
URI: nmdc:img_identifiers
"},{"location":"img_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$
name: img_identifiers\ndescription: A list of identifiers that relate the biosample to records in the IMG\n database.\ntitle: IMG Identifiers\ntodos:\n- add is_a or mixin modeling, like other external_database_identifiers\n- what class would IMG records belong to?! Are they Studies, Biosamples, or something\n else?\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nalias: img_identifiers\ndomain_of:\n- MetagenomeAnnotation\n- Biosample\n- MetatranscriptomeAnnotation\n- MetatranscriptomeExpressionAnalysis\n- MagsAnalysis\nrange: external_identifier\nmultivalued: true\npattern: ^img\\.taxon:[a-zA-Z0-9_][a-zA-Z0-9_\\/\\.]*$\n\none or more combinations of other DataObjects that can be analyzed together
URI: nmdc:in_manifest
"},{"location":"in_manifest/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"in_manifest/#properties","title":"Properties","text":"Range: Manifest
Multivalued: True
name: in_manifest\ndescription: one or more combinations of other DataObjects that can be analyzed together\ncomments:\n- A DataObject can be part of multiple manifests, for example, a DataObject could\n be part of a manifest for a single run of an instrument and a manifest for technical\n replicates of a single sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: in_manifest\ndomain_of:\n- DataObject\nrange: Manifest\nmultivalued: true\nstructured_pattern:\n syntax: ^{id_nmdc_prefix}:manif-{id_shoulder}-{id_blade}$\n interpolated: true\n\nURI: nmdc:inchi
"},{"location":"inchi/#properties","title":"Properties","text":"name: inchi\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi\nrange: string\n\nURI: nmdc:inchi_key
"},{"location":"inchi_key/#properties","title":"Properties","text":"name: inchi_key\nnotes:\n- 'key set to false due to rare collisions: Pletnev I, Erin A, McNaught A, Blinov\n K, Tchekhovskoi D, Heller S (2012) InChIKey collision resistance: an experimental\n testing. J Cheminform. 4:12'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: inchi_key\nrange: string\n\nA distinguishable space within a structure, the purpose for which discrete areas of a building is used
URI: MIXS:0000763
"},{"location":"indoor_space/#inheritance","title":"Inheritance","text":"name: indoor_space\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A distinguishable space within a structure, the purpose for which discrete\n areas of a building is used\ntitle: indoor space\nexamples:\n- value: foyer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor space\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000763\nalias: indoor_space\ndomain_of:\n- Biosample\nrange: indoor_space_enum\nmultivalued: false\n\nType of indoor surface
URI: MIXS:0000764
"},{"location":"indoor_surf/#inheritance","title":"Inheritance","text":"name: indoor_surf\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Type of indoor surface\ntitle: indoor surface\nexamples:\n- value: wall\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- indoor surface\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000764\nalias: indoor_surf\ndomain_of:\n- Biosample\nrange: indoor_surf_enum\nmultivalued: false\n\nPercentage of industrial effluents received by wastewater treatment plant
URI: MIXS:0000662
"},{"location":"indust_eff_percent/#inheritance","title":"Inheritance","text":"name: indust_eff_percent\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Percentage of industrial effluents received by wastewater treatment plant\ntitle: industrial effluent percent\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- industrial effluent percent\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000662\nalias: indust_eff_percent\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe amount of time it takes to complete each infiltration activity
URI: nmdc:infiltrations
"},{"location":"infiltrations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"infiltrations/#properties","title":"Properties","text":"Range: String
Multivalued: True
Regex pattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$
name: infiltrations\ndescription: The amount of time it takes to complete each infiltration activity\nexamples:\n- value: '[''00:01:32'', ''00:00:53'']'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.protocols.io/view/field-sampling-protocol-kqdg3962pg25/v1\naliases:\n- infiltration_1\n- infiltration_2\nrank: 1000\nlist_elements_ordered: true\nalias: infiltrations\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\npattern: ^(?:[0-9]|[1-9][0-9]|9[0-9]|0[0-9]|0[0-5][0-9]):[0-5][0-9]:[0-5][0-9]$\n\nConcentration of particles such as sand, grit, metal particles, ceramics, etc.; can include multiple particles
URI: MIXS:0000664
"},{"location":"inorg_particles/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: inorg_particles\nannotations:\n expected_value:\n tag: expected_value\n value: inorganic particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of particles such as sand, grit, metal particles, ceramics,\n etc.; can include multiple particles\ntitle: inorganic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inorganic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000664\nalias: inorg_particles\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe nucleotide base count number of input reads for QC analysis.
URI: nmdc:input_base_count
"},{"location":"input_base_count/#inheritance","title":"Inheritance","text":"name: input_base_count\ndescription: The nucleotide base count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_base_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nTotal number of input contigs.
URI: nmdc:input_contig_num
"},{"location":"input_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"input_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: input_contig_num\ndescription: Total number of input contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nTotal mass of sample used in activity.
URI: nmdc:input_mass
"},{"location":"input_mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Extraction A material separation in which a desired component of an input material is se... no"},{"location":"input_mass/#properties","title":"Properties","text":"name: input_mass\ndescription: Total mass of sample used in activity.\ntitle: sample mass used\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample mass\n- sample weight\nexact_mappings:\n- MS:1000004\nnarrow_mappings:\n- MIXS:0000111\nrank: 1000\nalias: input_mass\ndomain_of:\n- Extraction\nrange: QuantityValue\n\n_TODO _
URI: nmdc:input_read_bases
"},{"location":"input_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"input_read_bases/#properties","title":"Properties","text":"name: input_read_bases\ndescription: 'TODO '\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_read_bases\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nThe sequence count number of input reads for QC analysis.
URI: nmdc:input_read_count
"},{"location":"input_read_count/#inheritance","title":"Inheritance","text":"name: input_read_count\ndescription: The sequence count number of input reads for QC analysis.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: input_read_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nThe volume of the input sample.
URI: nmdc:input_volume
"},{"location":"input_volume/#properties","title":"Properties","text":"name: input_volume\ndescription: The volume of the input sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: input_volume\nrange: QuantityValue\n\nURI: nmdc:insdc_analysis_identifiers
"},{"location":"insdc_analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$
name: insdc_analysis_identifiers\ncomments:\n- in INSDC this is a run but it corresponds to a GOLD analysis\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/runs/DRR218479\n description: Illumina MiSeq paired end sequencing of SAMD00212331\n- value: https://www.ebi.ac.uk/ena/browser/view/ERR436051\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RR[0-9]{6,}$\n\nURI: nmdc:insdc_assembly_identifiers
"},{"location":"insdc_assembly_identifiers/#inheritance","title":"Inheritance","text":"Range: String
Regex pattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$
name: insdc_assembly_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: assembly_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_assembly_identifiers\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: string\npattern: ^insdc.sra:[A-Z]+[0-9]+(\\.[0-9]+)?$\n\nidentifiers for corresponding project in INSDC Bioproject
URI: nmdc:insdc_bioproject_identifiers
"},{"location":"insdc_bioproject_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$
name: insdc_bioproject_identifiers\ndescription: identifiers for corresponding project in INSDC Bioproject\ncomments:\n- these are distinct IDs from INSDC SRA/ENA project identifiers, but are usually(?)\n one to one\nexamples:\n- value: https://bioregistry.io/bioproject:PRJNA366857\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ncbi.nlm.nih.gov/bioproject/\n- https://www.ddbj.nig.ac.jp/bioproject/index-e.html\naliases:\n- NCBI bioproject identifiers\n- DDBJ bioproject identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_bioproject_identifiers\ndomain_of:\n- NucleotideSequencing\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^bioproject:PRJ[DEN][A-Z][0-9]+$\n\nidentifiers for corresponding sample in INSDC
URI: nmdc:insdc_biosample_identifiers
"},{"location":"insdc_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$
name: insdc_biosample_identifiers\ndescription: identifiers for corresponding sample in INSDC\nexamples:\n- value: https://bioregistry.io/biosample:SAMEA5989477\n- value: https://bioregistry.io/biosample:SAMD00212331\n description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/108\n- https://www.ebi.ac.uk/biosamples/\n- https://www.ncbi.nlm.nih.gov/biosample\n- https://www.ddbj.nig.ac.jp/biosample/index-e.html\naliases:\n- EBI biosample identifiers\n- NCBI biosample identifiers\n- DDBJ biosample identifiers\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^biosample:SAM[NED]([A-Z])?[0-9]+$\n\nURI: nmdc:insdc_experiment_identifiers
"},{"location":"insdc_experiment_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$
name: insdc_experiment_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_experiment_identifiers\ndomain_of:\n- NucleotideSequencing\n- DataObject\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RX[0-9]{6,}$\n\nAny identifier covered by the International Nucleotide Sequence Database Collaboration
URI: nmdc:insdc_identifiers
"},{"location":"insdc_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain insdc_sra_ena_study_identifiers identifiers for corresponding project in INSDC SRA / ENA None insdc_bioproject_identifiers identifiers for corresponding project in INSDC Bioproject None Study, NucleotideSequencing insdc_biosample_identifiers identifiers for corresponding sample in INSDC None Biosample insdc_secondary_sample_identifiers secondary identifiers for corresponding sample in INSDC None insdc_experiment_identifiers None DataObject, NucleotideSequencing insdc_analysis_identifiers None insdc_assembly_identifiers None MetagenomeAssembly, MetatranscriptomeAssembly"},{"location":"insdc_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: insdc_identifiers\ndescription: Any identifier covered by the International Nucleotide Sequence Database\n Collaboration\ncomments:\n- note that we deliberately abstract over which of the partner databases accepted\n the initial submission\n- 'the first letter of the accession indicates which partner accepted the initial\n submission: E for ENA, D for DDBJ, or S or N for NCBI.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.insdc.org/\n- https://ena-docs.readthedocs.io/en/latest/submit/general-guide/accessions.html\naliases:\n- EBI identifiers\n- NCBI identifiers\n- DDBJ identifiers\nrank: 1000\nmixin: true\nalias: insdc_identifiers\nrange: string\n\nsecondary identifiers for corresponding sample in INSDC
URI: nmdc:insdc_secondary_sample_identifiers
"},{"location":"insdc_secondary_sample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^biosample:(E|D|S)RS[0-9]{6,}$
name: insdc_secondary_sample_identifiers\ndescription: secondary identifiers for corresponding sample in INSDC\ncomments:\n- ENA redirects these to primary IDs, e.g. https://www.ebi.ac.uk/ena/browser/view/DRS166340\n -> SAMD00212331\n- MGnify uses these as their primary sample IDs\nexamples:\n- value: https://bioregistry.io/insdc.sra:DRS166340\n description: I13_N_5-10 sample from Soil fungal diversity along elevational gradients\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_secondary_sample_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^biosample:(E|D|S)RS[0-9]{6,}$\n\nidentifiers for corresponding project in INSDC SRA / ENA
URI: nmdc:insdc_sra_ena_study_identifiers
"},{"location":"insdc_sra_ena_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$
name: insdc_sra_ena_study_identifiers\ndescription: identifiers for corresponding project in INSDC SRA / ENA\nexamples:\n- value: https://bioregistry.io/insdc.sra:SRP121659\n description: Avena fatua rhizosphere microbial communities - H1_Rhizo_Litter_2 metatranscriptome\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/bioregistry/bioregistry/issues/109\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\n- https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies\naliases:\n- EBI ENA study identifiers\n- NCBI SRA identifiers\n- DDBJ SRA identifiers\nrank: 1000\nis_a: study_identifiers\nmixins:\n- insdc_identifiers\nalias: insdc_sra_ena_study_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^insdc.sra:(E|D|S)RP[0-9]{6,}$\n\nThe recorded value at sampling time (power density)
URI: MIXS:0000168
"},{"location":"inside_lux/#inheritance","title":"Inheritance","text":"name: inside_lux\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatt per square metre\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded value at sampling time (power density)\ntitle: inside lux light\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- inside lux light\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000168\nalias: inside_lux\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThis property links a database object to the set of instruments within it.
URI: nmdc:instrument_set
"},{"location":"instrument_set/#inheritance","title":"Inheritance","text":"Range: Instrument
Multivalued: True
name: instrument_set\ndescription: This property links a database object to the set of instruments within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: instrument_set\ndomain_of:\n- Database\nrange: Instrument\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nWhat instrument was used during DataGeneration or MaterialProcessing.
URI: nmdc:instrument_used
"},{"location":"instrument_used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no FiltrationProcess The process of segregation of phases; e no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no LibraryPreparation no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no DataGeneration The methods and processes used to generate omics data from a biosample or org... no Extraction A material separation in which a desired component of an input material is se... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no"},{"location":"instrument_used/#properties","title":"Properties","text":"Range: Instrument
Multivalued: True
name: instrument_used\ndescription: What instrument was used during DataGeneration or MaterialProcessing.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: instrument_used\ndomain_of:\n- MaterialProcessing\n- DataGeneration\nrange: Instrument\nmultivalued: true\n\nThe physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas
URI: MIXS:0000813
"},{"location":"int_wall_cond/#inheritance","title":"Inheritance","text":"name: int_wall_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the wall at the time of sampling; photos or\n video preferred; use drawings to indicate location of damaged areas\ntitle: interior wall condition\nexamples:\n- value: damaged\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- interior wall condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000813\nalias: int_wall_cond\ndomain_of:\n- Biosample\nrange: int_wall_cond_enum\nmultivalued: false\n\nwhether internal calibration was used, if false, external calibration was used
URI: nmdc:internal_calibration
"},{"location":"internal_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CalibrationInformation A calibration object that is associated with a process yes"},{"location":"internal_calibration/#properties","title":"Properties","text":"name: internal_calibration\ndescription: whether internal calibration was used, if false, external calibration\n was used\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: internal_calibration\ndomain_of:\n- CalibrationInformation\nrange: boolean\n\nfield describing aspect of the investigation/study to which the sample belongs
Note
This is an abstract slot and should not be populated directly.
URI: nmdc:investigation_field
"},{"location":"investigation_field/#inheritance","title":"Inheritance","text":"name: investigation field\ndescription: field describing aspect of the investigation/study to which the sample\n belongs\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: investigation_field\ndomain_of:\n- Biosample\nrange: string\n\nThe ionization source used to introduce processed samples into a mass spectrometer
URI: nmdc:ionization_source
"},{"location":"ionization_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"ionization_source/#properties","title":"Properties","text":"name: ionization_source\ndescription: The ionization source used to introduce processed samples into a mass\n spectrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1000008\nrank: 1000\nalias: ionization_source\ndomain_of:\n- MassSpectrometryConfiguration\nrange: IonizationSourceEnum\n\nWhether or not pressure was applied to a thing or process.
URI: nmdc:is_pressurized
"},{"location":"is_pressurized/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"is_pressurized/#properties","title":"Properties","text":"name: is_pressurized\ndescription: Whether or not pressure was applied to a thing or process.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_pressurized\ndomain_of:\n- FiltrationProcess\nrange: boolean\n\nIs the (RNA) library stranded or non-stranded (unstranded).
URI: nmdc:is_stranded
"},{"location":"is_stranded/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"is_stranded/#properties","title":"Properties","text":"name: is_stranded\ndescription: Is the (RNA) library stranded or non-stranded (unstranded).\ncomments:\n- A value of true means the library is stranded, flase means non-stranded.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: is_stranded\ndomain_of:\n- LibraryPreparation\nrange: boolean\n\nList isotope exposure or addition applied to your sample.
URI: nmdc:isotope_exposure
"},{"location":"isotope_exposure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"isotope_exposure/#properties","title":"Properties","text":"Range: String
Recommended: True
name: isotope_exposure\ndescription: List isotope exposure or addition applied to your sample.\ntitle: isotope exposure/addition\ntodos:\n- Can we make the H218O correctly super and subscripted?\ncomments:\n- This is required when your experimental design includes the use of isotopically\n labeled compounds\nexamples:\n- value: 13C glucose\n- value: 18O water\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000751\nrank: 16\nalias: isotope_exposure\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nInjection water breakthrough date per well following a secondary and/or tertiary recovery
URI: MIXS:0001010
"},{"location":"iw_bt_date_well/#inheritance","title":"Inheritance","text":"name: iw_bt_date_well\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Injection water breakthrough date per well following a secondary and/or\n tertiary recovery\ntitle: injection water breakthrough date of specific well\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water breakthrough date of specific well\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001010\nalias: iw_bt_date_well\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nProportion of the produced fluids derived from injected water at the time of sampling. (e.g. 87%)
URI: MIXS:0000455
"},{"location":"iwf/#inheritance","title":"Inheritance","text":"name: iwf\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Proportion of the produced fluids derived from injected water at the\n time of sampling. (e.g. 87%)\ntitle: injection water fraction\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- injection water fraction\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000455\nalias: iwf\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nidentifiers for corresponding analysis projects in JGI Portal
URI: nmdc:jgi_portal_analysis_project_identifiers
"},{"location":"jgi_portal_analysis_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^jgi.analysis:[0-9]+$
Instances of this class should have identifiers with one of the following prefixes:
name: jgi_portal_analysis_project_identifiers\nid_prefixes:\n- jgi.analysis\ndescription: identifiers for corresponding analysis projects in JGI Portal\nexamples:\n- value: https://data.jgi.doe.gov/search?q=1414320\n description: Metagenome - Draft Assembly YELL_051-M-20210705-comp-DNA1\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- jgi_portal_identifiers\nalias: jgi_portal_analysis_project_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^jgi.analysis:[0-9]+$\n\nidentifiers for entities according to JGI Portal
URI: nmdc:jgi_portal_identifiers
"},{"location":"jgi_portal_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain jgi_portal_study_identifiers Identifiers that link a NMDC study to a website hosting raw and analyzed data... None Study jgi_portal_analysis_project_identifiers identifiers for corresponding analysis projects in JGI Portal None"},{"location":"jgi_portal_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: jgi_portal_identifiers\ndescription: identifiers for entities according to JGI Portal\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://data.jgi.doe.gov/\nrank: 1000\nmixin: true\nalias: jgi_portal_identifiers\nrange: string\n\nIdentifiers that link a NMDC study to a website hosting raw and analyzed data for a JGI proposal. The suffix of the curie can used to query the GOLD API and is interoperable with an award DOI from OSTI and a GOLD study identifier.
URI: nmdc:jgi_portal_study_identifiers
"},{"location":"jgi_portal_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^jgi.proposal:\\d+$
Instances of this class should have identifiers with one of the following prefixes:
name: jgi_portal_study_identifiers\nid_prefixes:\n- jgi.proposal\ndescription: Identifiers that link a NMDC study to a website hosting raw and analyzed\n data for a JGI proposal. The suffix of the curie can used to query the GOLD API\n and is interoperable with an award DOI from OSTI and a GOLD study identifier.\ntitle: JGI Portal Study identifiers\ncomments:\n- Could this could be considered a related identifier?\n- Curie suffix is the Site Award Number from an OSTI award page\n- Site Award Number 507130 == award doi doi:10.46936/10.25585/60000017 -- GOLD study\n identifier gold:Gs0154044\n- bioregistry.io/jgi.proposal:507130 ==https://genome.jgi.doe.gov/portal/BioDefcarcycling/BioDefcarcycling.info.html\nexamples:\n- value: jgi.proposal:507130\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- jgi_portal_identifiers\nalias: jgi_portal_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^jgi.proposal:\\d+$\n\nThe substance from which a portion was taken.
URI: nmdc:known_as
"},{"location":"known_as/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"known_as/#properties","title":"Properties","text":"name: known_as\ndescription: The substance from which a portion was taken.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: known_as\ndomain_of:\n- PortionOfSubstance\nrange: ChemicalEntityEnum\n\nShould use ISO 639-1 code e.g. \"en\", \"fr\"
URI: nmdc:language
"},{"location":"language/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextValue A basic string value no"},{"location":"language/#properties","title":"Properties","text":"name: language\ndescription: Should use ISO 639-1 code e.g. \"en\", \"fr\"\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: language\ndomain_of:\n- TextValue\nrange: language_code\n\nThe last time the floor was cleaned (swept, mopped, vacuumed)
URI: MIXS:0000814
"},{"location":"last_clean/#inheritance","title":"Inheritance","text":"name: last_clean\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The last time the floor was cleaned (swept, mopped, vacuumed)\ntitle: last time swept/mopped/vacuumed\nexamples:\n- value: 2018-05-11:T14:30Z\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- last time swept/mopped/vacuumed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000814\nalias: last_clean\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system
URI: MIXS:0000009
"},{"location":"lat_lon/#inheritance","title":"Inheritance","text":"name: lat_lon\nannotations:\n expected_value:\n tag: expected_value\n value: decimal degrees, limit to 8 decimal points\ndescription: The geographical origin of the sample as defined by latitude and longitude.\n The values should be reported in decimal degrees and in WGS84 system\ntitle: geographic location (latitude and longitude)\nexamples:\n- value: 50.586825 6.408977\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- geographic location (latitude and longitude)\nrank: 1000\nis_a: environment field\nstring_serialization: '{float} {float}'\nslot_uri: MIXS:0000009\nalias: lat_lon\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: GeolocationValue\nmultivalued: false\n\nlatitude
URI: wgs84:lat
"},{"location":"latitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"latitude/#properties","title":"Properties","text":"name: latitude\ndescription: latitude\nexamples:\n- value: '-33.460524'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:latitude\nrank: 1000\nslot_uri: wgs84:lat\nalias: latitude\ndomain_of:\n- GeolocationValue\nrange: decimal_degree\n\nlime buffer capacity, determined after 30 minute incubation
URI: nmdc:lbc_thirty
"},{"location":"lbc_thirty/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lbc_thirty/#properties","title":"Properties","text":"name: lbc_thirty\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\ndescription: lime buffer capacity, determined after 30 minute incubation\ntitle: lime buffer capacity (at 30 minutes)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n pH unit\nexamples:\n- value: 543 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\n- https://secure.caes.uga.edu/extension/publications/files/pdf/C%20874_5.PDF\naliases:\n- lbc_thirty\n- lbc30\n- lime buffer capacity (at 30 minutes)\nrank: 1000\nalias: lbc_thirty\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nlime buffer capacity, determined at equilibrium after 5 day incubation
URI: nmdc:lbceq
"},{"location":"lbceq/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"lbceq/#properties","title":"Properties","text":"name: lbceq\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ppm CaCO3/pH\n occurrence:\n tag: occurrence\n value: '1'\ndescription: lime buffer capacity, determined at equilibrium after 5 day incubation\ntitle: lime buffer capacity (after 5 day incubation)\ncomments:\n- This is the mass of lime, in mg, needed to raise the pH of one kg of soil by one\n pH unit\nexamples:\n- value: 1575 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- lbceq\n- lime buffer capacity (at 5-day equilibrium)\nrank: 1000\nalias: lbceq\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nURI: nmdc:library_preparation_kit
"},{"location":"library_preparation_kit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_preparation_kit/#properties","title":"Properties","text":"name: library_preparation_kit\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_preparation_kit\ndomain_of:\n- LibraryPreparation\nrange: string\n\nURI: nmdc:library_type
"},{"location":"library_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"library_type/#properties","title":"Properties","text":"name: library_type\ntitle: library type\nexamples:\n- value: DNA\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: library_type\ndomain_of:\n- LibraryPreparation\nrange: LibraryTypeEnum\n\nMeasurement of light intensity
URI: MIXS:0000706
"},{"location":"light_intensity/#inheritance","title":"Inheritance","text":"name: light_intensity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: lux\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of light intensity\ntitle: light intensity\nexamples:\n- value: 0.3 lux\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light intensity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000706\nalias: light_intensity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment(s) involving exposure to light, including both light intensity and quality.
URI: MIXS:0000569
"},{"location":"light_regm/#inheritance","title":"Inheritance","text":"name: light_regm\nannotations:\n expected_value:\n tag: expected_value\n value: exposure type;light intensity;light quality\n preferred_unit:\n tag: preferred_unit\n value: lux; micrometer, nanometer, angstrom\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about treatment(s) involving exposure to light, including\n both light intensity and quality.\ntitle: light regimen\nexamples:\n- value: incandescant light;10 lux;450 nanometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000569\nalias: light_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nApplication of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light
URI: MIXS:0000769
"},{"location":"light_type/#inheritance","title":"Inheritance","text":"Range: LightTypeEnum
Multivalued: True
name: light_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Application of light to achieve some practical or aesthetic effect. Lighting\n includes the use of both artificial light sources such as lamps and light fixtures,\n as well as natural illumination by capturing daylight. Can also include absence\n of light\ntitle: light type\nexamples:\n- value: desk lamp\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- light type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000769\nalias: light_type\ndomain_of:\n- Biosample\nrange: light_type_enum\nmultivalued: true\n\nLink to additional analysis results performed on the sample
URI: MIXS:0000340
"},{"location":"link_addit_analys/#inheritance","title":"Inheritance","text":"name: link_addit_analys\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to additional analysis results performed on the sample\ntitle: links to additional analysis\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- links to additional analysis\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000340\nalias: link_addit_analys\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nLink to digitized soil maps or other soil classification information
URI: MIXS:0000329
"},{"location":"link_class_info/#inheritance","title":"Inheritance","text":"name: link_class_info\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to digitized soil maps or other soil classification information\ntitle: link to classification information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to classification information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000329\nalias: link_class_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nLink to climate resource
URI: MIXS:0000328
"},{"location":"link_climate_info/#inheritance","title":"Inheritance","text":"name: link_climate_info\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Link to climate resource\ntitle: link to climate information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- link to climate information\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000328\nalias: link_climate_info\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nHydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000990
"},{"location":"lithology/#inheritance","title":"Inheritance","text":"name: lithology\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Hydrocarbon resource main lithology (Additional information: http://petrowiki.org/Lithology_and_rock_type_determination).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: lithology\nexamples:\n- value: Volcanic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000990\nalias: lithology\ndomain_of:\n- Biosample\nrange: lithology_enum\nmultivalued: false\n\nSoil classification based on local soil classification system
URI: MIXS:0000330
"},{"location":"local_class/#inheritance","title":"Inheritance","text":"name: local_class\nannotations:\n expected_value:\n tag: expected_value\n value: local classification name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Soil classification based on local soil classification system\ntitle: soil_taxonomic/local classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000330\nalias: local_class\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\nReference or method used in determining the local soil classification
URI: MIXS:0000331
"},{"location":"local_class_meth/#inheritance","title":"Inheritance","text":"name: local_class_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the local soil classification\ntitle: soil_taxonomic/local classification method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil_taxonomic/local classification method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000331\nalias: local_class_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:location
"},{"location":"location/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"location/#properties","title":"Properties","text":"name: location\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: location\ndomain_of:\n- Biosample\nrange: string\n\nlongitude
URI: wgs84:long
"},{"location":"longitude/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GeolocationValue A normalized value for a location on the earth's surface yes"},{"location":"longitude/#properties","title":"Properties","text":"name: longitude\ndescription: longitude\nexamples:\n- value: '150.168149'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- schema:longitude\nrank: 1000\nslot_uri: wgs84:long\nalias: longitude\ndomain_of:\n- GeolocationValue\nrange: decimal_degree\n\nNumber of contigs which were excluded from binning for depth of coverage.
URI: nmdc:low_depth_contig_num
"},{"location":"low_depth_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"low_depth_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: low_depth_contig_num\ndescription: Number of contigs which were excluded from binning for depth of coverage.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: low_depth_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nConcentration of magnesium in the sample
URI: MIXS:0000431
"},{"location":"magnesium/#inheritance","title":"Inheritance","text":"name: magnesium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per liter, milligram per liter, parts per million, micromole per kilogram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of magnesium in the sample\ntitle: magnesium\nexamples:\n- value: 52.8 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- magnesium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000431\nalias: magnesium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nContains detailed information about each metagenome-assembled genome.
URI: nmdc:mags_list
"},{"location":"mags_list/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"mags_list/#properties","title":"Properties","text":"Range: MagBin
Multivalued: True
name: mags_list\ndescription: Contains detailed information about each metagenome-assembled genome.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mags_list\ndomain_of:\n- MagsAnalysis\nrange: MagBin\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe nmdc-schema is a framework for describing multi-omics microbiome experiments and the data they produce. We aim to answer questions like:
All metadata gathered and stored by the NMDC community must validate against the NMDC Schema.
"},{"location":"maintaining-the-schema/#the-nmdc-schema-is-expressed-in-the-linkml-modeling-language","title":"The NMDC Schema is expressed in the LinkML modeling language.","text":"LinkML uses structures like classes, slots (for relationships and properties), types and enumerations to create a blueprint of the NMDC data. The schema is used to define the structure of the data, and to ensure that the data is consistent and interoperable. The schema is expressed in a human-readable format, and with the help of LinkML tooling, can be generated in multiple formats, including JSONSchema (used to support validation on ingest to NMDC), YAML (for ease of editing), and OWL. LinkML schemas generally make good use of terminology and concepts already modeled in external, trusted knowledge centers, especially ontologies, and especially those from the OBO Foundry.
Reuse of existing terminologies and knowledge can be found in several places in the NMDC schema, including the use of the MIxS schema, the EnvO ontology, and the CHEBI ontology. In addition, the NMDC schema elements like slots and classes are annotated with mappings (exact, narrow, related scopes) to these external resources.
For example:
doi_value:\n description: >-\n A digital object identifier, which is intended to persistantly identify some resource on the web.\n required: true\n aliases:\n - DOI\n - digital object identifier\n range: uriorcurie\n pattern: '^doi:10.\\d{2,9}/.*$'\n examples:\n - value: doi:10.46936/10.25585/60000880\n description: The DOI links to an electronic document.\n exact_mappings:\n - OBI:0002110\n narrow_mappings:\n - edam.data:1188\nOne consequence of this semantic/linked data orientation is that all schema elements are identified by a URI, most often in the compact CURIe form: a prefix and a local identifier. Even if a class isn't decorated with a class_uri annotation, it will always have a key (in a JSON, YAML or Python Obj sense), which is sometimes reiterated as the name. In that case, the class' URI will be <prefix>:<key>. LinkML schemas should have default prefix assertions, but any element can use a different prefix, as long as an expansion is provided.
Prefixes used in a LinkML must be associated with an expansion in the schema (which may include imported modules). Ideally, the expanded URI should be web resolvable, but that is not required. The prefixes can be expanded to base URIs owned by a particular resource, or they can be expanded to base URIs owned by some resolving service, like the bioregistry.
"},{"location":"maintaining-the-schema/#asserting-mappings-in-the-nmdc-schema","title":"Asserting mappings in the NMDC Schema","text":"As mentioned above, URIs are assigned to most elements of a LinkML schema, either explicitly by the schema authors, or implicitly through the default prefix and the element's key. If an external prefix is used, that means the semantics of the element are identical to the external term, unless otherwise refined. Sometimes it is desirable to associate a LinkML schema element with a term from an external resource, without asserting that the semantics are identical. In this case, a variety of mapping terms can be used.
Adding mappings to a schema element is one of the best and most compact ways to clarify the meaning of that element.
Schema contributors are strongly encouraged to use mappings whose prefixes are already defined in the schema. Schema contributors are always responsible for having a holistic understanding of an external term to be mapped into the schema. This means gaining familiarity with the parent and child terms, as well as any other axioms applied to the term. The EBI Ontology Lookup Service is a good place to look for these details.
When it appears necessary to use a mapping whose prefix isn't already defined in the schema, the contributor is responsible for having a holistic understanding of the external namespace (not just the term to be mapped). There are several ways to start assessing an ontology that is being considered as a source of mappings. If the ontology is in the OBO Foundry, one can look at the OBO Foundry Dashboard.
"},{"location":"maintaining-the-schema/#asserting-identifiers-in-linkml-data","title":"Asserting identifiers in LinkML data","text":"Generally speaking, the smallest atom of LinkML data is an instance of one class. LinkML slots take values, but always in the context of some class (on the right hand side). LinkML data files are frequently collections of instances of one or more classes. The is no requirement that these classes provide a slot whose value uniquely identifies the instances, but LinkML provides a mechanism that is broadly followed: one slot available in each class is annotated with identifier: true. (Or at least, that's what it would look like in a YAML serialization.) That means that the slot is required in all instances of the class, and that any collection of instances from that class must have unique values in that slot. It is also typical to say that the range of the is type uriorcurie.
A common pattern in the nmdc-schema is asserting that some identifiable process has inputs and outputs.
pooling_set:\n - id: pooling:1\n inputs:\n - biosample:1\n - biosample:2\n - biosample:3\n - id: pooling:2\n inputs:\n - biosample:4\n - biosample:5\n - biosample:6\nHere we have declared the existence of two pooling processes. A CURIe identifier is asserted for both of them, and three inputs are mentioned for each. The example CURIes above don't necessarily follow any nmdc-schema identifier pattern rules. If these were real CURIes, then the pooling and biosample prefixes would have to be defined in the schema files.
In this case, let's assume definitions for the biosample inputs should be defined elsewhere in an NMDC data set. Cases in which biosamples are mentioned without being defined would be considered violations of the referential integrity. The development of referential integrity validators for LinkML has begun in Autumn, 2023.
Another pattern is saying that something defined within a NMDC data set is equivalent to something defined elsewhere.
biosample_set:\n - id: biosample:1\n gold_biosample_identifiers:\n - gold:1\n - gold:2\nIn this case, the gold prefix must be defined in the schema. When expanded to URIs via the prefix definitions, these gold_biosample_identifiers would all be web-resolvable.
"},{"location":"maintaining-the-schema/#constraining-mentioned-identifiers","title":"Constraining mentioned identifiers","text":"We can limit the values that go into any slot by using a pattern constraint. We can also use the id_prefixes constraint to limit the prefixes that are used in whatever slot has been declared to be the identifier of a class. (Attributes of a class are supposed to be cascaded to subclasses, via the is_a attribute. This may not always be the case though. In the nmdc-schema we have been using a belt-and-suspenders approach of re-declaring the uriorcurie range )
All prefixes used in the id_prefixes constraint must be defined in the schema. We should have a standing practice of reflecting on the declared id_prefixes, and removing prefixes that haven't been used yet and are not likely to eer be used.
Maintenance of the prefix portions of a pattern will generally require more manual checking. We shouldn't be constraining the values of slots to use a prefix that isn't declared, but no checks are automatically applied.
Any class could use any slot with any range to \"link to\" something external. A Person could have a place_of_birth slot, and that could take unconstrained string or enumerated values like \"Switzerland\". But that doesn't provide much support for people looking up more information about the place_of_birth. You could create wikidata_place_of_birth and dbpedia_place_of_birth slots and add annotations to the slot to aid in external lookups, but that isn't a good practice if supporting several external targets. A better practice is to have one place_of_birth slot, with the uriorcuire range. Then users can provide values like <http://www.wikidata.org/entity/Q39> or <http://dbpedia.org/resource/Switzerland>. Then there is no ambiguity about the target of the link.
If the schema contains prefix definitions like wd: <http://www.wikidata.org/entity/> and dbpedia: <http://dbpedia.org/resource/>, then the values can be written as wd:Q39 and dbpedia:Switzerland. This is more compact and readable, but it requires that the prefixes be defined in the schema. Then, more constraint can be imposed with a pattern on the place_of_birth slot like '^(wd|dbpedia):.+$'
make gen-project)default_curi_maps any more--emsl-biosample-uuid-replacement in anyuri-strings-to-irispatterns and id_prefixeswarning Schema maps prefix 'CHEMBL.COMPOUND' to namespace 'https://bioregistry.io/chembl.compound:' instead of namespace 'http://identifiers.org/chembl.compound/' (canonical_prefixes)
warning Schema maps prefix 'rdf' to namespace 'http://www.w3.org/1999/02/22-rdf-syntax-ns#' instead of using prefix ' RDF' (canonical_prefixes) warning Schema maps prefix 'rdfs' to namespace 'http://www.w3.org/2000/01/rdf-schema#' instead of using prefix 'RDFS' ( canonical_prefixes)
"},{"location":"maintaining-the-schema/#typecodes","title":"Typecodes","text":"Not only does NMDC require the use of the nmdc prefix in the primary identifier for data instances, but we also define a pattern that the local portion of the ids must follow. For example, an example id from the NamedThing class is 'nmdc:mgmag-00-x012.1_7_c1'. The text that comes immediately after the nmdc prefix and colon, and before the first hyphen is the typecode, mgmag in this case. Typecodes must correspond 1:1 to a class in the NMDC schema. The typecodes currently in use are available from the nmdc-runtime API: https://api.microbiomedata.org/nmdcschema/typecodes
Please see identifers for more information on the minting of identifiers in NMDC directly, and for more discussion on identifier resolution and harmonization in NMDC.
"},{"location":"manganese/","title":"Slot: manganese (manganese)","text":"Concentration of manganese in the sample
URI: nmdc:manganese
"},{"location":"manganese/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"manganese/#properties","title":"Properties","text":"name: manganese\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of manganese in the sample\ntitle: manganese\nexamples:\n- value: 24.7 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- manganese\nrank: 1000\nalias: manganese\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nThe type of context in which the constituent DataObjects can be analyzed together.
URI: nmdc:manifest_category
"},{"location":"manifest_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Manifest A qualified collection of DataObjects that can be analyzed together in the sa... no"},{"location":"manifest_category/#properties","title":"Properties","text":"Range: ManifestCategoryEnum
Required: True
name: manifest_category\ndescription: The type of context in which the constituent DataObjects can be analyzed\n together.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: manifest_category\ndomain_of:\n- Manifest\nrange: ManifestCategoryEnum\nrequired: true\n\nThis property links a database object to the set of manifests within it.
URI: nmdc:manifest_set
"},{"location":"manifest_set/#inheritance","title":"Inheritance","text":"Range: Manifest
Multivalued: True
name: manifest_set\ndescription: This property links a database object to the set of manifests within\n it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: manifest_set\ndomain_of:\n- Database\nrange: Manifest\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
URI: nmdc:mass
"},{"location":"mass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"mass/#properties","title":"Properties","text":"name: mass\ndescription: A physical quality that inheres in a bearer by virtue of the proportion\n of the bearer's amount of matter.\ntitle: mass\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- PATO:0000125\nrank: 1000\nalias: mass\ndomain_of:\n- SubSamplingProcess\n- PortionOfSubstance\nrange: QuantityValue\n\nThe kind of mass analyzer(s) used during the spectra collection.
URI: nmdc:mass_analyzers
"},{"location":"mass_analyzers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_analyzers/#properties","title":"Properties","text":"Range: MassAnalyzerEnum
Multivalued: True
name: mass_analyzers\ndescription: The kind of mass analyzer(s) used during the spectra collection.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1000443\nrank: 1000\nalias: mass_analyzers\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassAnalyzerEnum\nmultivalued: true\n\nMode of running a mass spectrometer method by which m/z ranges are selected and ions possibly fragment.
URI: nmdc:mass_spectrometry_acquisition_strategy
"},{"location":"mass_spectrometry_acquisition_strategy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_spectrometry_acquisition_strategy/#properties","title":"Properties","text":"name: mass_spectrometry_acquisition_strategy\ndescription: Mode of running a mass spectrometer method by which m/z ranges are selected\n and ions possibly fragment.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- MS:1003213\nrank: 1000\nalias: mass_spectrometry_acquisition_strategy\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassSpectrometryAcquisitionStrategyEnum\n\nIndicates whether mass spectra were collected in full profile, reduced profile, or centroid mode during acquisition.
URI: nmdc:mass_spectrum_collection_modes
"},{"location":"mass_spectrum_collection_modes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"mass_spectrum_collection_modes/#properties","title":"Properties","text":"Range: MassSpectrumCollectionModeEnum
Multivalued: True
name: mass_spectrum_collection_modes\ndescription: Indicates whether mass spectra were collected in full profile, reduced\n profile, or centroid mode during acquisition.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mass_spectrum_collection_modes\ndomain_of:\n- MassSpectrometryConfiguration\nrange: MassSpectrumCollectionModeEnum\nmultivalued: true\n\nA material processing in which components of an input material become segregated in space
URI: nmdc:material_component_separation
"},{"location":"material_component_separation/#properties","title":"Properties","text":"name: material_component_separation\ndescription: A material processing in which components of an input material become\n segregated in space\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: material_component_separation\nrange: string\n\nThis property links a database object to the set of material processing within it.
URI: nmdc:material_processing_set
"},{"location":"material_processing_set/#inheritance","title":"Inheritance","text":"Range: MaterialProcessing
Multivalued: True
name: material_processing_set\ndescription: This property links a database object to the set of material processing\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: material_processing_set\ndomain_of:\n- Database\nrange: MaterialProcessing\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe maximum amount of people allowed in the indoor environment
URI: MIXS:0000229
"},{"location":"max_occup/#inheritance","title":"Inheritance","text":"name: max_occup\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The maximum amount of people allowed in the indoor environment\ntitle: maximum occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- maximum occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000229\nalias: max_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMD5 checksum of file (pre-compressed)
URI: nmdc:md5_checksum
"},{"location":"md5_checksum/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no"},{"location":"md5_checksum/#properties","title":"Properties","text":"name: md5_checksum\ndescription: MD5 checksum of file (pre-compressed)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: md5_checksum\ndomain_of:\n- DataObject\nrange: string\n\nMeasurement of mean friction velocity
URI: MIXS:0000498
"},{"location":"mean_frict_vel/#inheritance","title":"Inheritance","text":"name: mean_frict_vel\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of mean friction velocity\ntitle: mean friction velocity\nexamples:\n- value: 0.5 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000498\nalias: mean_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of mean peak friction velocity
URI: MIXS:0000502
"},{"location":"mean_peak_frict_vel/#inheritance","title":"Inheritance","text":"name: mean_peak_frict_vel\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of mean peak friction velocity\ntitle: mean peak friction velocity\nexamples:\n- value: 1 meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean peak friction velocity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000502\nalias: mean_peak_frict_vel\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nmechanical structure: a moving structure
URI: MIXS:0000815
"},{"location":"mech_struc/#inheritance","title":"Inheritance","text":"name: mech_struc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'mechanical structure: a moving structure'\ntitle: mechanical structure\nexamples:\n- value: elevator\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical structure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000815\nalias: mech_struc\ndomain_of:\n- Biosample\nrange: mech_struc_enum\nmultivalued: false\n\nInformation about any mechanical damage exerted on the plant; can include multiple damages and sites
URI: MIXS:0001052
"},{"location":"mechanical_damage/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: mechanical_damage\nannotations:\n expected_value:\n tag: expected_value\n value: damage type;body site\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about any mechanical damage exerted on the plant; can include\n multiple damages and sites\ntitle: mechanical damage\nexamples:\n- value: pruning;bark\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mechanical damage\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{text}'\nslot_uri: MIXS:0001052\nalias: mechanical_damage\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nNames of the contigs that make up a metagenome-assembled genome.
URI: nmdc:members_id
"},{"location":"members_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"members_id/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: members_id\ndescription: Names of the contigs that make up a metagenome-assembled genome.\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- GENEPIO:0100596\nrank: 1000\nalias: members_id\ndomain_of:\n- MagBin\nrange: string\nmultivalued: true\n\nthe specific metabolite identifier
URI: nmdc:metabolite_identified
"},{"location":"metabolite_identified/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no"},{"location":"metabolite_identified/#properties","title":"Properties","text":"name: metabolite_identified\ndescription: the specific metabolite identifier\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metabolite_identified\ndomain_of:\n- MetaboliteIdentification\nrange: string\n\nThe identifier for the analysis activity that generated the functional annotation results, where the analysis activity is an instance of the/an appropriate subclass of WorkflowExecution
URI: nmdc:metagenome_annotation_id
","text":""},{"location":"metagenome_annotation_id/#properties","title":"Properties","text":"Range: WorkflowExecution
Required: True
name: metagenome_annotation_id\ndescription: The identifier for the analysis activity that generated the functional\n annotation results, where the analysis activity is an instance of the/an appropriate\n subclass of WorkflowExecution\ndeprecated: not used. 2024-10 https://github.com/microbiomedata/nmdc-schema/issues/1253\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metagenome_annotation_id\nrange: WorkflowExecution\nrequired: true\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:metagenome_assembly_parameter
"},{"location":"metagenome_assembly_parameter/#inheritance","title":"Inheritance","text":"name: metagenome_assembly_parameter\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: metagenome_assembly_parameter\nrange: string\n\nThe category of metaproteomics analysis being performed.
URI: nmdc:metaproteomics_analysis_category
"},{"location":"metaproteomics_analysis_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetaproteomicsAnalysis no"},{"location":"metaproteomics_analysis_category/#properties","title":"Properties","text":"Range: MetaproteomicsAnalysisCategoryEnum
Required: True
name: metaproteomics_analysis_category\ndescription: The category of metaproteomics analysis being performed.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: metaproteomics_analysis_category\ndomain_of:\n- MetaproteomicsAnalysis\nrange: MetaproteomicsAnalysisCategoryEnum\nrequired: true\n\nMethane (gas) amount or concentration at the time of sampling
URI: MIXS:0000101
"},{"location":"methane/#inheritance","title":"Inheritance","text":"name: methane\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, parts per billion, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Methane (gas) amount or concentration at the time of sampling\ntitle: methane\nexamples:\n- value: 1800 parts per billion\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- methane\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000101\nalias: methane\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:mgnify_analysis_identifiers
"},{"location":"mgnify_analysis_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: mgnify_analysis_identifiers\nnotes:\n- 'removed pattern: \"^mgnify:MGYA[0-9]+$\" ## TODO https://github.com/bioregistry/bioregistry/issues/109'\nexamples:\n- value: https://www.ebi.ac.uk/metagenomics/analyses/MGYA00002270\n description: combined analyses (taxonomic, functional) of sample ERS438107\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: analysis_identifiers\nmixins:\n- mgnify_identifiers\nalias: mgnify_analysis_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nURI: nmdc:mgnify_identifiers
"},{"location":"mgnify_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain mgnify_project_identifiers identifiers for corresponding project in MGnify None Study mgnify_analysis_identifiers None"},{"location":"mgnify_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: mgnify_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ebi.ac.uk/metagenomics/\nrank: 1000\nmixin: true\nalias: mgnify_identifiers\nrange: string\n\nidentifiers for corresponding project in MGnify
URI: nmdc:mgnify_project_identifiers
"},{"location":"mgnify_project_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^mgnify.proj:[A-Z]+[0-9]+$
name: mgnify_project_identifiers\ndescription: identifiers for corresponding project in MGnify\nexamples:\n- value: https://bioregistry.io/mgnify.proj:MGYS00005757\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- mgnify_identifiers\nalias: mgnify_project_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^mgnify.proj:[A-Z]+[0-9]+$\n\nReference or method used in determining microbial biomass carbon
URI: nmdc:micro_biomass_c_meth
"},{"location":"micro_biomass_c_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_c_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: micro_biomass_c_meth\ndescription: Reference or method used in determining microbial biomass carbon\ntitle: microbial biomass carbon method\ntodos:\n- How should we separate values? | or ;? lets be consistent\ncomments:\n- required if \"microbial_biomass_c\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000339\nrank: 11\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_c_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nReference or method used in determining microbial biomass
URI: MIXS:0000339
"},{"location":"micro_biomass_meth/#inheritance","title":"Inheritance","text":"name: micro_biomass_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining microbial biomass\ntitle: microbial biomass method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000339\nalias: micro_biomass_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nReference or method used in determining microbial biomass nitrogen
URI: nmdc:micro_biomass_n_meth
"},{"location":"micro_biomass_n_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"micro_biomass_n_meth/#properties","title":"Properties","text":"name: micro_biomass_n_meth\ndescription: Reference or method used in determining microbial biomass nitrogen\ntitle: microbial biomass nitrogen method\ncomments:\n- required if \"microbial_biomass_n\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(87)90052-6\n- value: https://doi.org/10.1016/0038-0717(87)90052-6 | https://www.sciencedirect.com/science/article/abs/pii/0038071787900526\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000339\nrank: 13\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: micro_biomass_n_meth\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units
URI: MIXS:0000650
"},{"location":"microbial_biomass/#inheritance","title":"Inheritance","text":"name: microbial_biomass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: ton, kilogram, gram per kilogram soil\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer. If you keep this, you would need to have correction\n factors used for conversion to the final units\ntitle: microbial biomass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- microbial biomass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000650\nalias: microbial_biomass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.
URI: nmdc:microbial_biomass_c
"},{"location":"microbial_biomass_c/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_c/#properties","title":"Properties","text":"name: microbial_biomass_c\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer.\ntitle: microbial biomass carbon\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n method are required\nexamples:\n- value: 0.05 ug C/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 10\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_c\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThe part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer.
URI: nmdc:microbial_biomass_n
"},{"location":"microbial_biomass_n/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"microbial_biomass_n/#properties","title":"Properties","text":"name: microbial_biomass_n\ndescription: The part of the organic matter in the soil that constitutes living microorganisms\n smaller than 5-10 micrometer.\ntitle: microbial biomass nitrogen\ncomments:\n- If you provide this, correction factors used for conversion to the final units and\n method are required\nexamples:\n- value: 0.05 ug N/g dry soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 12\nstring_serialization: '{float} {unit}'\nalias: microbial_biomass_n\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nThis document provides guidance on how to migrate from one version of the NMDC Schema to another.
smallest Q-Value associated with the peptide sequence as provided by MSGFPlus tool
URI: nmdc:min_q_value
","text":""},{"location":"min_q_value/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"min_q_value/#properties","title":"Properties","text":"name: min_q_value\ndescription: smallest Q-Value associated with the peptide sequence as provided by\n MSGFPlus tool\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- OBI:0001442\nrank: 1000\nalias: min_q_value\ndomain_of:\n- PeptideQuantification\nrange: float\n\nInformation about treatment involving the use of mineral supplements; should include the name of mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple mineral nutrient regimens
URI: MIXS:0000570
"},{"location":"mineral_nutr_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: mineral_nutr_regm\nannotations:\n expected_value:\n tag: expected_value\n value: mineral nutrient name;mineral nutrient amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the use of mineral supplements;\n should include the name of mineral nutrient, amount administered, treatment regimen\n including how many times the treatment was repeated, how long each treatment lasted,\n and the start and end time of the entire treatment; can include multiple mineral\n nutrient regimens\ntitle: mineral nutrient regimen\nexamples:\n- value: potassium;15 gram;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000570\nalias: mineral_nutr_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAny other measurement performed or parameter collected, that is not listed here
URI: MIXS:0000752
"},{"location":"misc_param/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: misc_param\nannotations:\n expected_value:\n tag: expected_value\n value: parameter name;measurement value\n occurrence:\n tag: occurrence\n value: m\ndescription: Any other measurement performed or parameter collected, that is not listed\n here\ntitle: miscellaneous parameter\nexamples:\n- value: Bicarbonate ion concentration;2075 micromole per kilogram\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- miscellaneous parameter\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000752\nalias: misc_param\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe last date on which the database information was modified.
URI: nmdc:mod_date
"},{"location":"mod_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Biosample Biological source material which can be characterized by an experiment no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"mod_date/#properties","title":"Properties","text":"name: mod_date\ndescription: The last date on which the database information was modified.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: mod_date\ndomain_of:\n- Biosample\n- DataGeneration\nrange: string\n\nURI: nmdc:model
"},{"location":"model/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Instrument A material entity that is designed to perform a function in a scientific inve... no"},{"location":"model/#properties","title":"Properties","text":"name: model\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: model\ndomain_of:\n- Instrument\nrange: InstrumentModelEnum\n\nThe type of modification being done
URI: nmdc:modifier_substance
"},{"location":"modifier_substance/#properties","title":"Properties","text":"name: modifier_substance\ndescription: The type of modification being done\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: modifier_substance\nrange: string\n\nConcentration of n-alkanes; can include multiple n-alkanes
URI: MIXS:0000503
"},{"location":"n_alkanes/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: n_alkanes\nannotations:\n expected_value:\n tag: expected_value\n value: n-alkane name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of n-alkanes; can include multiple n-alkanes\ntitle: n-alkanes\nexamples:\n- value: n-hexadecane;100 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- n-alkanes\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000503\nalias: n_alkanes\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA human readable label for an entity
URI: nmdc:name
"},{"location":"name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MetabolomicsAnalysis no Study A study summarizes the overall goal of a research initiative and outlines the... yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no Site no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... no GeneProduct A molecule encoded by a gene that has an evolved function no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no CalibrationInformation A calibration object that is associated with a process no FiltrationProcess The process of segregation of phases; e no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no ProcessedSample no MetatranscriptomeAnnotation no Biosample Biological source material which can be characterized by an experiment no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no CollectingBiosamplesFromSite no MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no EnvironmentalMaterialTerm no MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... no Sample A sample is a material entity that can be characterized by an experiment no ChemicalEntity An atom or molecule that can be represented with a chemical formula no MaterialEntity no Instrument A material entity that is designed to perform a function in a scientific inve... no NamedThing a databased entity or concept/class no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no Manifest A qualified collection of DataObjects that can be analyzed together in the sa... no OrthologyGroup A set of genes or gene products in which all members are orthologous no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no OntologyClass A representation of class defined in an external ontology no Configuration A set of parameters that define the actions of a process and is shared among ... no PersonValue An attribute value representing a person yes ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no LibraryPreparation no Protocol no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... yes DataObject An object that primarily consists of symbols that represent information yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... yes DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"name/#properties","title":"Properties","text":"name: name\ndescription: A human readable label for an entity\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: name\ndomain_of:\n- PersonValue\n- NamedThing\n- Protocol\nrange: string\n\nComma delimited ordered list of NCBI taxonomy names.
URI: nmdc:ncbi_lineage
"},{"location":"ncbi_lineage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"ncbi_lineage/#properties","title":"Properties","text":"name: ncbi_lineage\ndescription: Comma delimited ordered list of NCBI taxonomy names.\ncomments:\n- Example root,cellular organisms,Eukaryota,Discoba,Euglenozoa,Diplonemea,Diplonemidae\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_lineage\ndomain_of:\n- EukEval\nrange: string\n\nDash-delimited ordered list of NCBI taxonomy identifiers (TaxId)
URI: nmdc:ncbi_lineage_tax_ids
"},{"location":"ncbi_lineage_tax_ids/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no"},{"location":"ncbi_lineage_tax_ids/#properties","title":"Properties","text":"Range: String
Regex pattern: ^\\d+(-\\d+)*$
name: ncbi_lineage_tax_ids\ndescription: Dash-delimited ordered list of NCBI taxonomy identifiers (TaxId)\ncomments:\n- Example 1-131567-2759-2611352-33682-191814-2603949\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_lineage_tax_ids\ndomain_of:\n- EukEval\nrange: string\npattern: ^\\d+(-\\d+)*$\n\nURI: nmdc:ncbi_project_name
"},{"location":"ncbi_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no"},{"location":"ncbi_project_name/#properties","title":"Properties","text":"name: ncbi_project_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_project_name\ndomain_of:\n- NucleotideSequencing\nrange: string\n\nURI: nmdc:ncbi_taxonomy_name
"},{"location":"ncbi_taxonomy_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"ncbi_taxonomy_name/#properties","title":"Properties","text":"name: ncbi_taxonomy_name\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: ncbi_taxonomy_name\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:neon_biosample_identifiers
"},{"location":"neon_biosample_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: neon_biosample_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: biosample_identifiers\nmixins:\n- neon_identifiers\nalias: neon_biosample_identifiers\ndomain_of:\n- Biosample\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nidentifiers for entities according to NEON
URI: nmdc:neon_identifiers
"},{"location":"neon_identifiers/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain neon_study_identifiers None Study neon_biosample_identifiers None Biosample"},{"location":"neon_identifiers/#properties","title":"Properties","text":"Range: String
Mixin: True
name: neon_identifiers\ndescription: identifiers for entities according to NEON\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: neon_identifiers\nrange: string\n\nURI: nmdc:neon_study_identifiers
"},{"location":"neon_study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: neon_study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: study_identifiers\nmixins:\n- neon_identifiers\nalias: neon_study_identifiers\ndomain_of:\n- Study\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nConcentration of nitrate in the sample
URI: MIXS:0000425
"},{"location":"nitrate/#inheritance","title":"Inheritance","text":"name: nitrate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrate in the sample\ntitle: nitrate\nexamples:\n- value: 65 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000425\nalias: nitrate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of nitrate nitrogen in the sample
URI: nmdc:nitrate_nitrogen
"},{"location":"nitrate_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrate_nitrogen/#properties","title":"Properties","text":"name: nitrate_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrate nitrogen in the sample\ntitle: nitrate_nitrogen\ncomments:\n- often below some specified limit of detection\nexamples:\n- value: 0.29 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrate_nitrogen\n- NO3-N\nrank: 1000\nalias: nitrate_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrite in the sample
URI: MIXS:0000426
"},{"location":"nitrite/#inheritance","title":"Inheritance","text":"name: nitrite\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrite in the sample\ntitle: nitrite\nexamples:\n- value: 0.5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrite\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000426\nalias: nitrite\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of nitrite nitrogen in the sample
URI: nmdc:nitrite_nitrogen
"},{"location":"nitrite_nitrogen/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"nitrite_nitrogen/#properties","title":"Properties","text":"name: nitrite_nitrogen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrite nitrogen in the sample\ntitle: nitrite_nitrogen\nexamples:\n- value: 1.2 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- nitrite_nitrogen\n- NO2-N\nrank: 1000\nalias: nitrite_nitrogen\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of nitrogen (total)
URI: MIXS:0000504
"},{"location":"nitro/#inheritance","title":"Inheritance","text":"name: nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of nitrogen (total)\ntitle: nitrogen\nexamples:\n- value: 4.2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000504\nalias: nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nAmount of biomass; should include the name for the part of biomass measured, e.g.insect, plant, total. Can include multiple measurements separated by ;
URI: nmdc:non_microb_biomass
"},{"location":"non_microb_biomass/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass/#properties","title":"Properties","text":"name: non_microb_biomass\ndescription: Amount of biomass; should include the name for the part of biomass measured,\n e.g.insect, plant, total. Can include multiple measurements separated by ;\ntitle: non-microbial biomass\nexamples:\n- value: insect 0.23 ug; plant 1g\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000174\n- MIXS:0000650\nrank: 8\nstring_serialization: '{text};{float} {unit}'\nalias: non_microb_biomass\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nReference or method used in determining biomass
URI: nmdc:non_microb_biomass_method
"},{"location":"non_microb_biomass_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"non_microb_biomass_method/#properties","title":"Properties","text":"name: non_microb_biomass_method\ndescription: Reference or method used in determining biomass\ntitle: non-microbial biomass method\ncomments:\n- required if \"non-microbial biomass\" is provided\nexamples:\n- value: https://doi.org/10.1038/s41467-021-26181-3\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000650\nrank: 9\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: non_microb_biomass_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nInformation about treatment involving the exposure of plant to non-mineral nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral nutrient, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple non-mineral nutrient regimens
URI: MIXS:0000571
"},{"location":"non_min_nutr_regm/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
name: non_min_nutr_regm\nannotations:\n expected_value:\n tag: expected_value\n value: non-mineral nutrient name;non-mineral nutrient amount;treatment interval\n and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving the exposure of plant to non-mineral\n nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral\n nutrient, amount administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple non-mineral nutrient regimens\ntitle: non-mineral nutrient regimen\nexamples:\n- value: carbon dioxide;10 mole per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- non-mineral nutrient regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000571\nalias: non_min_nutr_regm\ndomain_of:\n- Biosample\nrange: string\nmultivalued: true\n\nURI: nmdc:notes
"},{"location":"notes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"notes/#properties","title":"Properties","text":"name: notes\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: notes\ndomain_of:\n- Study\nrange: string\n\nA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids
URI: MIXS:0000038
"},{"location":"nucl_acid_amp/#inheritance","title":"Inheritance","text":"name: nucl_acid_amp\nannotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of\n specific nucleic acids\ntitle: nucleic acid amplification\nexamples:\n- value: https://phylogenomics.me/protocols/16s-pcr-protocol/\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid amplification\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000038\nalias: nucl_acid_amp\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\nA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample
URI: MIXS:0000037
"},{"location":"nucl_acid_ext/#inheritance","title":"Inheritance","text":"name: nucl_acid_ext\nannotations:\n expected_value:\n tag: expected_value\n value: PMID, DOI or URL\ndescription: A link to a literature reference, electronic resource or a standard operating\n procedure (SOP), that describes the material separation to recover the nucleic acid\n fraction from a sample\ntitle: nucleic acid extraction\nexamples:\n- value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- nucleic acid extraction\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000037\nalias: nucl_acid_ext\nrange: TextValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:nucleic_acid_sequence_source_field
"},{"location":"nucleic_acid_sequence_source_field/#inheritance","title":"Inheritance","text":"name: nucleic acid sequence source field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: nucleic_acid_sequence_source_field\ndomain_of:\n- Biosample\nrange: string\n\nNumber of 16s sequences detected, a subunit of prokaryotic ribosomes.
URI: nmdc:num_16s
"},{"location":"num_16s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_16s/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: num_16s\ndescription: Number of 16s sequences detected, a subunit of prokaryotic ribosomes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- NCIT:C105370\nrank: 1000\nalias: num_16s\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nNumber of 23 seqeuences detected, a subunit of ribosomes.
URI: nmdc:num_23s
"},{"location":"num_23s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_23s/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: num_23s\ndescription: Number of 23 seqeuences detected, a subunit of ribosomes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OMIT:0013245\nrank: 1000\nalias: num_23s\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nNumber of 5s seqeuences detected, a subunit of ribosomes.
URI: nmdc:num_5s
"},{"location":"num_5s/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_5s/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: num_5s\ndescription: Number of 5s seqeuences detected, a subunit of ribosomes.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- OMIT:0013248\nrank: 1000\nalias: num_5s\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nThe sequence count number of input reads aligned to assembled contigs.
URI: nmdc:num_aligned_reads
"},{"location":"num_aligned_reads/#inheritance","title":"Inheritance","text":"name: num_aligned_reads\ndescription: The sequence count number of input reads aligned to assembled contigs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_aligned_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sequence count number of input reads for assembly.
URI: nmdc:num_input_reads
"},{"location":"num_input_reads/#inheritance","title":"Inheritance","text":"name: num_input_reads\ndescription: The sequence count number of input reads for assembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: num_input_reads\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nNumber of transfer transfer RNAs.
URI: nmdc:num_t_rna
"},{"location":"num_t_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"num_t_rna/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: num_t_rna\ndescription: Number of transfer transfer RNAs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nbroad_mappings:\n- NCIT:C816\nrank: 1000\nalias: num_t_rna\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nNumber of contigs
URI: nmdc:number_of_contig
"},{"location":"number_of_contig/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"number_of_contig/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: number_of_contig\ndescription: Number of contigs\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- GENEPIO:0000093\nrank: 1000\nalias: number_of_contig\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nThe number of pets residing in the sampled space
URI: MIXS:0000231
"},{"location":"number_pets/#inheritance","title":"Inheritance","text":"name: number_pets\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of pets residing in the sampled space\ntitle: number of pets\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of pets\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000231\nalias: number_pets\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of plant(s) in the sampling space
URI: MIXS:0000230
"},{"location":"number_plants/#inheritance","title":"Inheritance","text":"name: number_plants\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of plant(s) in the sampling space\ntitle: number of houseplants\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of houseplants\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000230\nalias: number_plants\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe number of individuals currently occupying in the sampling location
URI: MIXS:0000232
"},{"location":"number_resident/#inheritance","title":"Inheritance","text":"name: number_resident\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of individuals currently occupying in the sampling location\ntitle: number of residents\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- number of residents\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000232\nalias: number_resident\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:object
"},{"location":"object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyRelation A relationship between two ontology classes as specified either directly in t... no"},{"location":"object/#properties","title":"Properties","text":"Range: OntologyClass
Required: True
name: object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: object\nowner: OntologyRelation\ndomain_of:\n- OntologyRelation\nrange: OntologyClass\nrequired: true\n\nApplies to a property that links a database object to a set of objects. This is necessary in a json document to provide context for a list, and to allow for a single json object that combines multiple object types
URI: nmdc:object_set
"},{"location":"object_set/#mixin-usage","title":"Mixin Usage","text":"mixed into description range domain chemical_entity_set This property links a database object to the set of chemical entities within ... None ontology_class_set This property links a database object to the set of ontology classes within i... OntologyClass biosample_set This property links a database object to the set of samples within it Biosample Database study_set This property links a database object to the set of studies within it Study Database field_research_site_set FieldResearchSite Database collecting_biosamples_from_site_set CollectingBiosamplesFromSite Database data_object_set This property links a database object to the set of data objects within it DataObject Database genome_feature_set This property links a database object to the set of all features GenomeFeature Database functional_annotation_set This property links a database object to the set of all functional annotation... FunctionalAnnotation Database workflow_execution_set This property links a database object to the set of workflow executions WorkflowExecution Database data_generation_set This property links a database object to the set of data generations within i... DataGeneration Database processed_sample_set This property links a database object to the set of processed samples within ... ProcessedSample Database instrument_set This property links a database object to the set of instruments within it Instrument Database calibration_set This property links a database object to the set of calibrations within it CalibrationInformation Database configuration_set This property links a database object to the set of configurations within it Configuration Database manifest_set This property links a database object to the set of manifests within it Manifest Database protocol_execution_set This property links a database object to the set of protocol executions withi... ProtocolExecution Database storage_process_set This property links a database object to the set of storage processes within ... StorageProcess Database material_processing_set This property links a database object to the set of material processing withi... MaterialProcessing Database"},{"location":"object_set/#properties","title":"Properties","text":"Range: String
Multivalued: True
Mixin: True
name: object_set\ndescription: Applies to a property that links a database object to a set of objects.\n This is necessary in a json document to provide context for a list, and to allow\n for a single json object that combines multiple object types\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixin: true\nalias: object_set\nrange: string\nmultivalued: true\ninlined_as_list: true\n\nThe scientific objectives associated with the entity. It SHOULD correspond to scientific norms for objectives field in a structured abstract.
URI: nmdc:objective
"},{"location":"objective/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"objective/#properties","title":"Properties","text":"name: objective\ndescription: The scientific objectives associated with the entity. It SHOULD correspond\n to scientific norms for objectives field in a structured abstract.\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- SIO:000337\nrank: 1000\nalias: objective\ndomain_of:\n- Study\nrange: string\n\nAverage number of occupants at time of sampling per square footage
URI: MIXS:0000217
"},{"location":"occup_density_samp/#inheritance","title":"Inheritance","text":"name: occup_density_samp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Average number of occupants at time of sampling per square footage\ntitle: occupant density at sampling\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupant density at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000217\nalias: occup_density_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of documentation of occupancy
URI: MIXS:0000816
"},{"location":"occup_document/#inheritance","title":"Inheritance","text":"name: occup_document\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of documentation of occupancy\ntitle: occupancy documentation\nexamples:\n- value: estimate\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy documentation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000816\nalias: occup_document\ndomain_of:\n- Biosample\nrange: occup_document_enum\nmultivalued: false\n\nNumber of occupants present at time of sample within the given space
URI: MIXS:0000772
"},{"location":"occup_samp/#inheritance","title":"Inheritance","text":"name: occup_samp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Number of occupants present at time of sample within the given space\ntitle: occupancy at sampling\nexamples:\n- value: '10'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- occupancy at sampling\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000772\nalias: occup_samp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:omics_processing_identifiers
"},{"location":"omics_processing_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: omics_processing_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: omics_processing_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nThe type of omics data
URI: nmdc:omics_type
","text":""},{"location":"omics_type/#properties","title":"Properties","text":"name: omics_type\ndescription: The type of omics data\ndeprecated: 'True'\nexamples:\n- value: metatranscriptome\n- value: metagenome\nfrom_schema: https://w3id.org/nmdc/nmdc\ndeprecated_element_has_exact_replacement: analyte_category\nrank: 1000\nalias: omics_type\nrange: string\n\nThis property links a database object to the set of ontology classes within it.
URI: nmdc:ontology_class_set
"},{"location":"ontology_class_set/#inheritance","title":"Inheritance","text":"Range: OntologyClass
Multivalued: True
name: ontology_class_set\ndescription: This property links a database object to the set of ontology classes\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: ontology_class_set\nrange: OntologyClass\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe ORCID of a person.
URI: nmdc:orcid
"},{"location":"orcid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person yes"},{"location":"orcid/#properties","title":"Properties","text":"name: orcid\ndescription: The ORCID of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: orcid\ndomain_of:\n- PersonValue\nrange: string\n\nThe solution(s) that moves through a chromatography column.
URI: nmdc:ordered_mobile_phases
"},{"location":"ordered_mobile_phases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no"},{"location":"ordered_mobile_phases/#properties","title":"Properties","text":"Range: MobilePhaseSegment
Multivalued: True
name: ordered_mobile_phases\ndescription: The solution(s) that moves through a chromatography column.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nlist_elements_ordered: true\nalias: ordered_mobile_phases\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: MobilePhaseSegment\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of organic carbon
URI: MIXS:0000508
"},{"location":"org_carb/#inheritance","title":"Inheritance","text":"name: org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic carbon\ntitle: organic carbon\nexamples:\n- value: 1.5 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000508\nalias: org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nIf qpcr was used for the cell count, the target gene name, the primer sequence and the cycling conditions should also be provided. (Example: 16S rrna; FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min; annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min; 30 cycles)
URI: MIXS:0000099
"},{"location":"org_count_qpcr_info/#inheritance","title":"Inheritance","text":"name: org_count_qpcr_info\nannotations:\n expected_value:\n tag: expected_value\n value: gene name;FWD:forward primer sequence;REV:reverse primer sequence;initial\n denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles\n preferred_unit:\n tag: preferred_unit\n value: number of cells per gram (or ml or cm^2)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'If qpcr was used for the cell count, the target gene name, the primer\n sequence and the cycling conditions should also be provided. (Example: 16S rrna;\n FWD:ACGTAGCTATGACGT REV:GTGCTAGTCGAGTAC; initial denaturation:90C_5min; denaturation:90C_2min;\n annealing:52C_30 sec; elongation:72C_30 sec; 90 C for 1 min; final elongation:72C_5min;\n 30 cycles)'\ntitle: organism count qPCR information\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count qPCR information\nrank: 1000\nis_a: core field\nstring_serialization: '{text};FWD:{dna};REV:{dna};initial denaturation:degrees_minutes;denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes; total cycles'\nslot_uri: MIXS:0000099\nalias: org_count_qpcr_info\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nConcentration of organic matter
URI: MIXS:0000204
"},{"location":"org_matter/#inheritance","title":"Inheritance","text":"name: org_matter\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic matter\ntitle: organic matter\nexamples:\n- value: 1.75 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000204\nalias: org_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of organic nitrogen
URI: MIXS:0000205
"},{"location":"org_nitro/#inheritance","title":"Inheritance","text":"name: org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of organic nitrogen\ntitle: organic nitrogen\nexamples:\n- value: 4 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000205\nalias: org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMethod used for obtaining organic nitrogen
URI: nmdc:org_nitro_method
"},{"location":"org_nitro_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"org_nitro_method/#properties","title":"Properties","text":"name: org_nitro_method\ndescription: Method used for obtaining organic nitrogen\ntitle: organic nitrogen method\ncomments:\n- required if \"org_nitro\" is provided\nexamples:\n- value: https://doi.org/10.1016/0038-0717(85)90144-0\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000338\n- MIXS:0000205\nrank: 14\nstring_serialization: '{PMID}|{DOI}|{URL}'\nalias: org_nitro_method\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\n\nConcentration of particles such as faeces, hairs, food, vomit, paper fibers, plant material, humus, etc.
URI: MIXS:0000665
"},{"location":"org_particles/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: org_particles\nannotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of particles such as faeces, hairs, food, vomit, paper\n fibers, plant material, humus, etc.\ntitle: organic particles\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organic particles\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000665\nalias: org_particles\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTotal cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)
URI: MIXS:0000103
"},{"location":"organism_count/#inheritance","title":"Inheritance","text":"Range: QuantityValue
Multivalued: True
name: organism_count\nannotations:\n expected_value:\n tag: expected_value\n value: organism name;measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: number of cells per cubic meter, number of cells per milliliter, number\n of cells per cubic centimeter\n occurrence:\n tag: occurrence\n value: m\ndescription: 'Total cell count of any organism (or group of organisms) per gram, volume\n or area of sample, should include name of organism followed by count. The method\n that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided.\n (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'\ntitle: organism count\nexamples:\n- value: total prokaryotes;3.5e7 cells per milliliter;qPCR\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- organism count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000103\nalias: organism_count\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nOther treatments applied to your samples that are not applicable to the provided fields
URI: nmdc:other_treatment
"},{"location":"other_treatment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"other_treatment/#properties","title":"Properties","text":"Range: String
Recommended: True
name: other_treatment\ndescription: Other treatments applied to your samples that are not applicable to the\n provided fields\ntitle: other treatments\nnotes:\n- Values entered here will be used to determine potential new slots.\ncomments:\n- This is an open text field to provide any treatments that cannot be captured in\n the provided slots.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000300\nrank: 15\nstring_serialization: '{text}'\nalias: other_treatment\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nAfter QC analysis nucleotide base count number.
URI: nmdc:output_base_count
"},{"location":"output_base_count/#inheritance","title":"Inheritance","text":"name: output_base_count\ndescription: After QC analysis nucleotide base count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_base_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nTODO
URI: nmdc:output_read_bases
"},{"location":"output_read_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no"},{"location":"output_read_bases/#properties","title":"Properties","text":"name: output_read_bases\ndescription: TODO\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: output_read_bases\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nAfter QC analysis sequence count number.
URI: nmdc:output_read_count
"},{"location":"output_read_count/#inheritance","title":"Inheritance","text":"name: output_read_count\ndescription: After QC analysis sequence count number.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: read_qc_analysis_statistic\nalias: output_read_count\ndomain_of:\n- ReadQcAnalysis\nrange: float\n\nDepth of the original oil water contact (OWC) zone (average) (m TVDSS)
URI: MIXS:0000405
"},{"location":"owc_tvdss/#inheritance","title":"Inheritance","text":"name: owc_tvdss\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Depth of the original oil water contact (OWC) zone (average) (m TVDSS)\ntitle: oil water contact depth\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oil water contact depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000405\nalias: owc_tvdss\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nOxygenation status of sample
URI: MIXS:0000753
"},{"location":"oxy_stat_samp/#inheritance","title":"Inheritance","text":"name: oxy_stat_samp\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oxygenation status of sample\ntitle: oxygenation status of sample\nexamples:\n- value: aerobic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygenation status of sample\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000753\nalias: oxy_stat_samp\ndomain_of:\n- Biosample\nrange: oxy_stat_samp_enum\nmultivalued: false\n\nOxygen (gas) amount or concentration at the time of sampling
URI: MIXS:0000104
"},{"location":"oxygen/#inheritance","title":"Inheritance","text":"name: oxygen\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oxygen (gas) amount or concentration at the time of sampling\ntitle: oxygen\nexamples:\n- value: 600 parts per million\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- oxygen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000104\nalias: oxygen\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nLinks a resource to another resource that either logically or physically includes it.
URI: dcterms:isPartOf
"},{"location":"part_of/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected yes Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"part_of/#properties","title":"Properties","text":"Range: NamedThing
Multivalued: True
name: part_of\ndescription: Links a resource to another resource that either logically or physically\n includes it.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- is part of\nrank: 1000\nslot_uri: dcterms:isPartOf\nalias: part_of\ndomain_of:\n- FieldResearchSite\n- Study\nrange: NamedThing\nmultivalued: true\n\nConcentration of particulate organic carbon
URI: MIXS:0000515
"},{"location":"part_org_carb/#inheritance","title":"Inheritance","text":"name: part_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of particulate organic carbon\ntitle: particulate organic carbon\nexamples:\n- value: 1.92 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000515\nalias: part_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of particulate organic nitrogen
URI: MIXS:0000719
"},{"location":"part_org_nitro/#inheritance","title":"Inheritance","text":"name: part_org_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of particulate organic nitrogen\ntitle: particulate organic nitrogen\nexamples:\n- value: 0.3 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particulate organic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000719\nalias: part_org_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nParticles are classified, based on their size, into six general categories:clay, silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded by the name of the particle type; can include multiple values
URI: MIXS:0000206
"},{"location":"particle_class/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: particle_class\nannotations:\n expected_value:\n tag: expected_value\n value: particle name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: m\ndescription: Particles are classified, based on their size, into six general categories:clay,\n silt, sand, gravel, cobbles, and boulders; should include amount of particle preceded\n by the name of the particle type; can include multiple values\ntitle: particle classification\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- particle classification\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000206\nalias: particle_class\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nDescription of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'
URI: MIXS:0000049
"},{"location":"pcr_cond/#inheritance","title":"Inheritance","text":"name: pcr_cond\nannotations:\n expected_value:\n tag: expected_value\n value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\ndescription: Description of reaction conditions and components of PCR in the form\n of 'initial denaturation:94degC_1.5min; annealing=...'\ntitle: pcr conditions\nexamples:\n- value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr conditions\nrank: 1000\nis_a: sequencing field\nstring_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final\n elongation:degrees_minutes;total cycles\nslot_uri: MIXS:0000049\nalias: pcr_cond\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:pcr_cycles
"},{"location":"pcr_cycles/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"pcr_cycles/#properties","title":"Properties","text":"name: pcr_cycles\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- OBI:0002475\nrank: 1000\nalias: pcr_cycles\ndomain_of:\n- LibraryPreparation\nrange: integer\n\nPCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters
URI: MIXS:0000046
"},{"location":"pcr_primers/#inheritance","title":"Inheritance","text":"name: pcr_primers\nannotations:\n expected_value:\n tag: expected_value\n value: 'FWD: forward primer sequence;REV:reverse primer sequence'\ndescription: PCR primers that were used to amplify the sequence of the targeted gene,\n locus or subfragment. This field should contain all the primers used for a single\n PCR reaction if multiple forward or reverse primers are present in a single PCR\n reaction. The primer sequence should be reported in uppercase letters\ntitle: pcr primers\nexamples:\n- value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pcr primers\nrank: 1000\nis_a: sequencing field\nstring_serialization: FWD:{dna};REV:{dna}\nslot_uri: MIXS:0000046\nalias: pcr_primers\ndomain_of:\n- LibraryPreparation\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:peptide_sequence
","text":""},{"location":"peptide_sequence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sequence/#properties","title":"Properties","text":"name: peptide_sequence\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence\ndomain_of:\n- PeptideQuantification\nrange: string\n\ncount of peptide sequences grouped to the best_protein
URI: nmdc:peptide_sequence_count
","text":""},{"location":"peptide_sequence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"peptide_sequence_count/#properties","title":"Properties","text":"name: peptide_sequence_count\ndescription: count of peptide sequences grouped to the best_protein\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sequence_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\nsum of filter passing MS2 spectra associated with the peptide sequence within a given LC-MS/MS data file
URI: nmdc:peptide_spectral_count
","text":""},{"location":"peptide_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_spectral_count/#properties","title":"Properties","text":"name: peptide_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the peptide sequence\n within a given LC-MS/MS data file\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_spectral_count\ndomain_of:\n- PeptideQuantification\nrange: integer\n\ncombined MS1 extracted ion chromatograms derived from MS2 spectra associated with the peptide sequence from a given LC-MS/MS data file using the MASIC tool
URI: nmdc:peptide_sum_masic_abundance
","text":""},{"location":"peptide_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no"},{"location":"peptide_sum_masic_abundance/#properties","title":"Properties","text":"name: peptide_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n with the peptide sequence from a given LC-MS/MS data file using the MASIC tool\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: peptide_sum_masic_abundance\ndomain_of:\n- PeptideQuantification\nrange: integer\n\nMeasure of the ability of a hydrocarbon resource to allow fluids to pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))
URI: MIXS:0000404
"},{"location":"permeability/#inheritance","title":"Inheritance","text":"name: permeability\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: mD\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Measure of the ability of a hydrocarbon resource to allow fluids to\n pass through it. (Additional information: https://en.wikipedia.org/wiki/Permeability_(earth_sciences))'\ntitle: permeability\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- permeability\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} - {integer} {unit}'\nslot_uri: MIXS:0000404\nalias: permeability\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nType of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types
URI: MIXS:0000754
"},{"location":"perturbation/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: perturbation\nannotations:\n expected_value:\n tag: expected_value\n value: perturbation type name;perturbation interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Type of perturbation, e.g. chemical administration, physical disturbance,\n etc., coupled with perturbation regimen including how many times the perturbation\n was repeated, how long each perturbation lasted, and the start and end time of the\n entire perturbation period; can include multiple perturbation types\ntitle: perturbation\nexamples:\n- value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- perturbation\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000754\nalias: perturbation\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nInformation about treatment involving use of insecticides; should include the name of pesticide, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple pesticide regimens
URI: MIXS:0000573
"},{"location":"pesticide_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: pesticide_regm\nannotations:\n expected_value:\n tag: expected_value\n value: pesticide name;pesticide amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of insecticides; should include\n the name of pesticide, amount administered, treatment regimen including how many\n times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple pesticide regimens\ntitle: pesticide regimen\nexamples:\n- value: pyrethrum;0.6 milligram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pesticide regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000573\nalias: pesticide_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of petroleum hydrocarbon
URI: MIXS:0000516
"},{"location":"petroleum_hydrocarb/#inheritance","title":"Inheritance","text":"name: petroleum_hydrocarb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of petroleum hydrocarbon\ntitle: petroleum hydrocarbon\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- petroleum hydrocarbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000516\nalias: petroleum_hydrocarb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nPh measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid
URI: MIXS:0001001
"},{"location":"ph/#inheritance","title":"Inheritance","text":"name: ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ph measurement of the sample, or liquid portion of sample, or aqueous\n phase of the fluid\ntitle: pH\nexamples:\n- value: '7.2'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001001\nalias: ph\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\nReference or method used in determining ph
URI: MIXS:0001106
"},{"location":"ph_meth/#inheritance","title":"Inheritance","text":"name: ph_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining ph\ntitle: pH method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0001106\nalias: ph_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about treatment involving exposure of plants to varying levels of ph of the growth media, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimen
URI: MIXS:0001056
"},{"location":"ph_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: ph_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving exposure of plants to varying levels\n of ph of the growth media, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple regimen\ntitle: pH regimen\nexamples:\n- value: 7.6;R2/2018-05-11:T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pH regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001056\nalias: ph_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of phaeopigments; can include multiple phaeopigments
URI: MIXS:0000180
"},{"location":"phaeopigments/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: phaeopigments\nannotations:\n expected_value:\n tag: expected_value\n value: phaeopigment name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of phaeopigments; can include multiple phaeopigments\ntitle: phaeopigments\nexamples:\n- value: 2.5 milligram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phaeopigments\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000180\nalias: phaeopigments\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2.
URI: nmdc:phase
"},{"location":"phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"phase/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
Maximum Value: 2
name: phase\ndescription: The phase for a coding sequence entity. For example, phase of a CDS as\n represented in a GFF3 with a value of 0, 1 or 2.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:phase\nrank: 1000\nalias: phase\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 0\nmaximum_value: 2\n\nConcentration of phosphate
URI: MIXS:0000505
"},{"location":"phosphate/#inheritance","title":"Inheritance","text":"name: phosphate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of phosphate\ntitle: phosphate\nexamples:\n- value: 0.7 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000505\nalias: phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of phospholipid fatty acids; can include multiple values
URI: MIXS:0000181
"},{"location":"phosplipid_fatt_acid/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: phosplipid_fatt_acid\nannotations:\n expected_value:\n tag: expected_value\n value: phospholipid fatty acid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: mole per gram, mole per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of phospholipid fatty acids; can include multiple values\ntitle: phospholipid fatty acid\nexamples:\n- value: 2.98 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- phospholipid fatty acid\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000181\nalias: phosplipid_fatt_acid\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nMeasurement of photon flux
URI: MIXS:0000725
"},{"location":"photon_flux/#inheritance","title":"Inheritance","text":"name: photon_flux\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: number of photons per second per unit area\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of photon flux\ntitle: photon flux\nexamples:\n- value: 3.926 micromole photons per second per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- photon flux\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000725\nalias: photon_flux\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSpecification of the media for growing the plants or tissue cultured samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro liquid culture medium. Recommended value is a specific value from EO:plant growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or other controlled vocabulary
URI: MIXS:0001057
"},{"location":"plant_growth_med/#inheritance","title":"Inheritance","text":"name: plant_growth_med\nannotations:\n expected_value:\n tag: expected_value\n value: EO or enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specification of the media for growing the plants or tissue cultured\n samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in vitro\n liquid culture medium. Recommended value is a specific value from EO:plant growth\n medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147) or\n other controlled vocabulary\ntitle: plant growth medium\nexamples:\n- value: hydroponic plant culture media [EO:0007067]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant growth medium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001057\nalias: plant_growth_med\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nSubstance produced by the plant, where the sample was obtained from
URI: MIXS:0001058
"},{"location":"plant_product/#inheritance","title":"Inheritance","text":"name: plant_product\nannotations:\n expected_value:\n tag: expected_value\n value: product name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Substance produced by the plant, where the sample was obtained from\ntitle: plant product\nexamples:\n- value: xylem sap [PO:0025539]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant product\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001058\nalias: plant_product\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSex of the reproductive parts on the whole plant, e.g. pistillate, staminate, monoecieous, hermaphrodite.
URI: MIXS:0001059
"},{"location":"plant_sex/#inheritance","title":"Inheritance","text":"name: plant_sex\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sex of the reproductive parts on the whole plant, e.g. pistillate, staminate,\n monoecieous, hermaphrodite.\ntitle: plant sex\nexamples:\n- value: Hermaphroditic\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant sex\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001059\nalias: plant_sex\ndomain_of:\n- Biosample\nrange: plant_sex_enum\nmultivalued: false\n\nName of plant structure the sample was obtained from; for Plant Ontology (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO, e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex of it can be recorded here.
URI: MIXS:0001060
"},{"location":"plant_struc/#inheritance","title":"Inheritance","text":"name: plant_struc\nannotations:\n expected_value:\n tag: expected_value\n value: PO\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of plant structure the sample was obtained from; for Plant Ontology\n (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,\n e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the sex\n of it can be recorded here.\ntitle: plant structure\nexamples:\n- value: epidermis [PO:0005679]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- plant structure\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0001060\nalias: plant_struc\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nthe polarity of which ions are generated and detected
URI: nmdc:polarity_mode
"},{"location":"polarity_mode/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"polarity_mode/#properties","title":"Properties","text":"name: polarity_mode\ndescription: the polarity of which ions are generated and detected\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: polarity_mode\ndomain_of:\n- MassSpectrometryConfiguration\nrange: PolarityModeEnum\n\nPollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant
URI: MIXS:0000107
"},{"location":"pollutants/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: pollutants\nannotations:\n expected_value:\n tag: expected_value\n value: pollutant name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, mole per liter, milligram per liter, microgram per cubic meter\n occurrence:\n tag: occurrence\n value: m\ndescription: Pollutant types and, amount or concentrations measured at the time of\n sampling; can report multiple pollutants by entering numeric values preceded by\n name of pollutant\ntitle: pollutants\nexamples:\n- value: lead;0.15 microgram per cubic meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pollutants\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000107\nalias: pollutants\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nIndicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given
URI: MIXS:0000325
"},{"location":"pool_dna_extracts/#inheritance","title":"Inheritance","text":"name: pool_dna_extracts\nannotations:\n expected_value:\n tag: expected_value\n value: pooling status;number of pooled extracts\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Indicate whether multiple DNA extractions were mixed. If the answer yes,\n the number of extracts that were pooled should be given\ntitle: pooling of DNA extracts (if done)\nexamples:\n- value: yes;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pooling of DNA extracts (if done)\nrank: 1000\nis_a: core field\nstring_serialization: '{boolean};{integer}'\nslot_uri: MIXS:0000325\nalias: pool_dna_extracts\nrange: TextValue\nmultivalued: false\n\nPorosity of deposited sediment is volume of voids divided by the total volume of sample
URI: MIXS:0000211
"},{"location":"porosity/#inheritance","title":"Inheritance","text":"name: porosity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value or range\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Porosity of deposited sediment is volume of voids divided by the total\n volume of sample\ntitle: porosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- porosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000211\nalias: porosity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of potassium in the sample
URI: MIXS:0000430
"},{"location":"potassium/#inheritance","title":"Inheritance","text":"name: potassium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of potassium in the sample\ntitle: potassium\nexamples:\n- value: 463 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- potassium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000430\nalias: potassium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTemperature at which a liquid becomes semi solid and loses its flow characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a high paraffin content, typically found in crude deriving from a larger proportion of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)
URI: MIXS:0000127
"},{"location":"pour_point/#inheritance","title":"Inheritance","text":"name: pour_point\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Temperature at which a liquid becomes semi solid and loses its flow\n characteristics. In crude oil a high\u00ac\u2020pour point\u00ac\u2020is generally associated with a\n high paraffin content, typically found in crude deriving from a larger proportion\n of plant material. (soure: https://en.wikipedia.org/wiki/pour_point)'\ntitle: pour point\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pour point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000127\nalias: pour_point\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe process of pre-treatment removes materials that can be easily collected from the raw wastewater
URI: MIXS:0000348
"},{"location":"pre_treatment/#inheritance","title":"Inheritance","text":"name: pre_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: pre-treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process of pre-treatment removes materials that can be easily collected\n from the raw wastewater\ntitle: pre-treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pre-treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000348\nalias: pre_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:predicate
"},{"location":"predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyRelation A relationship between two ontology classes as specified either directly in t... no"},{"location":"predicate/#properties","title":"Properties","text":"Range: OntologyClass
Required: True
name: predicate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: predicate\nowner: OntologyRelation\ndomain_of:\n- OntologyRelation\nrange: OntologyClass\nrequired: true\n\nThe type and number of animals or insects present in the sampling space.
URI: MIXS:0000819
"},{"location":"pres_animal_insect/#inheritance","title":"Inheritance","text":"Range: String
Regex pattern: ^(cat|dog|rodent|snake|other);\\d+$
name: pres_animal_insect\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration;count\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type and number of animals or insects present in the sampling space.\ntitle: presence of pets, animals, or insects\nexamples:\n- value: cat;5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- presence of pets, animals, or insects\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000819\nalias: pres_animal_insect\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\npattern: ^(cat|dog|rodent|snake|other);\\d+$\n\nPressure to which the sample is subject to, in atmospheres
URI: MIXS:0000412
"},{"location":"pressure/#inheritance","title":"Inheritance","text":"name: pressure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: atmosphere\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Pressure to which the sample is subject to, in atmospheres\ntitle: pressure\nexamples:\n- value: 50 atmosphere\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000412\nalias: pressure\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining previous land use and dates
URI: MIXS:0000316
"},{"location":"prev_land_use_meth/#inheritance","title":"Inheritance","text":"name: prev_land_use_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining previous land use and dates\ntitle: history/previous land use method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000316\nalias: prev_land_use_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nPrevious land use and dates
URI: MIXS:0000315
"},{"location":"previous_land_use/#inheritance","title":"Inheritance","text":"name: previous_land_use\nannotations:\n expected_value:\n tag: expected_value\n value: land use name;date\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Previous land use and dates\ntitle: history/previous land use\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/previous land use\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{timestamp}'\nslot_uri: MIXS:0000315\nalias: previous_land_use\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMeasurement of primary production, generally measured as isotope uptake
URI: MIXS:0000728
"},{"location":"primary_prod/#inheritance","title":"Inheritance","text":"name: primary_prod\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per cubic meter per day, gram per square meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of primary production, generally measured as isotope uptake\ntitle: primary production\nexamples:\n- value: 100 milligram per cubic meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary production\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000728\nalias: primary_prod\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe process to produce both a generally homogeneous liquid capable of being treated biologically and a sludge that can be separately treated or processed
URI: MIXS:0000349
"},{"location":"primary_treatment/#inheritance","title":"Inheritance","text":"name: primary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: primary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process to produce both a generally homogeneous liquid capable of\n being treated biologically and a sludge that can be separately treated or processed\ntitle: primary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- primary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000349\nalias: primary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nPrincipal Investigator who led the study and/or generated the dataset.
URI: nmdc:principal_investigator
"},{"location":"principal_investigator/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataGeneration The methods and processes used to generate omics data from a biosample or org... no Study A study summarizes the overall goal of a research initiative and outlines the... no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no"},{"location":"principal_investigator/#properties","title":"Properties","text":"name: principal_investigator\ndescription: Principal Investigator who led the study and/or generated the dataset.\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- PI\nrank: 1000\nalias: principal_investigator\ndomain_of:\n- Study\n- DataGeneration\nrange: PersonValue\n\nThis property links a database object to the set of processed samples within it.
URI: nmdc:processed_sample_set
"},{"location":"processed_sample_set/#inheritance","title":"Inheritance","text":"Range: ProcessedSample
Multivalued: True
name: processed_sample_set\ndescription: This property links a database object to the set of processed samples\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: processed_sample_set\ndomain_of:\n- Database\nrange: ProcessedSample\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe organization that processed the sample.
URI: nmdc:processing_institution
"},{"location":"processing_institution/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MetabolomicsAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no FiltrationProcess The process of segregation of phases; e no MetatranscriptomeAnnotation no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no CollectingBiosamplesFromSite no MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no LibraryPreparation no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"processing_institution/#properties","title":"Properties","text":"name: processing_institution\ndescription: The organization that processed the sample.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: processing_institution\ndomain_of:\n- PlannedProcess\nrange: ProcessingInstitutionEnum\n\nOil and/or gas production rates per well (e.g. 524 m3 / day)
URI: MIXS:0000452
"},{"location":"prod_rate/#inheritance","title":"Inheritance","text":"name: prod_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Oil and/or gas production rates per well (e.g. 524 m3 / day)\ntitle: production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000452\nalias: prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nDate of field's first production
URI: MIXS:0001008
"},{"location":"prod_start_date/#inheritance","title":"Inheritance","text":"name: prod_start_date\nannotations:\n expected_value:\n tag: expected_value\n value: timestamp\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Date of field's first production\ntitle: production start date\nexamples:\n- value: '2018-05-11'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- production start date\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001008\nalias: prod_start_date\ndomain_of:\n- Biosample\nrange: TimestampValue\nmultivalued: false\n\nA url that points to an image of a person.
URI: nmdc:profile_image_url
"},{"location":"profile_image_url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PersonValue An attribute value representing a person no"},{"location":"profile_image_url/#properties","title":"Properties","text":"name: profile_image_url\ndescription: A url that points to an image of a person.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: profile_image_url\ndomain_of:\n- PersonValue\nrange: string\n\nCross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas
URI: MIXS:0001084
"},{"location":"profile_position/#inheritance","title":"Inheritance","text":"name: profile_position\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Cross-sectional position in the hillslope where sample was collected.sample\n area position in relation to surrounding areas\ntitle: profile position\nexamples:\n- value: summit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- profile position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001084\nalias: profile_position\ndomain_of:\n- Biosample\nrange: profile_position_enum\nmultivalued: false\n\nProposal IDs or names associated with dataset
URI: nmdc:project_id
"},{"location":"project_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"project_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: project_id\ndescription: Proposal IDs or names associated with dataset\ntitle: project ID\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1\nstring_serialization: '{text}'\nalias: project_id\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nURI: nmdc:proport_woa_temperature
"},{"location":"proport_woa_temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proport_woa_temperature/#properties","title":"Properties","text":"name: proport_woa_temperature\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: proport_woa_temperature\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:proposal_dna
"},{"location":"proposal_dna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_dna/#properties","title":"Properties","text":"Range: String
Recommended: True
name: proposal_dna\ntitle: DNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_dna\ndomain_of:\n- Biosample\nslot_group: JGI-Metagenomics\nrange: string\nrecommended: true\n\nURI: nmdc:proposal_rna
"},{"location":"proposal_rna/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"proposal_rna/#properties","title":"Properties","text":"Range: String
Recommended: True
name: proposal_rna\ntitle: RNA proposal ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '504000'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 19\nstring_serialization: '{text}'\nalias: proposal_rna\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nsum of filter passing MS2 spectra associated with the best protein within a given LC-MS/MS data file
URI: nmdc:protein_spectral_count
","text":""},{"location":"protein_spectral_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_spectral_count/#properties","title":"Properties","text":"name: protein_spectral_count\ndescription: sum of filter passing MS2 spectra associated with the best protein within\n a given LC-MS/MS data file\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_spectral_count\ndomain_of:\n- ProteinQuantification\nrange: integer\n\ncombined MS1 extracted ion chromatograms derived from MS2 spectra associated with the best protein from a given LC-MS/MS data file using the MASIC tool
URI: nmdc:protein_sum_masic_abundance
","text":""},{"location":"protein_sum_masic_abundance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no"},{"location":"protein_sum_masic_abundance/#properties","title":"Properties","text":"name: protein_sum_masic_abundance\ndescription: combined MS1 extracted ion chromatograms derived from MS2 spectra associated\n with the best protein from a given LC-MS/MS data file using the MASIC tool\ndeprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protein_sum_masic_abundance\ndomain_of:\n- ProteinQuantification\nrange: integer\n\nURI: nmdc:protocol_execution_category
"},{"location":"protocol_execution_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ProtocolExecution A PlannedProces that has PlannedProcess parts no"},{"location":"protocol_execution_category/#properties","title":"Properties","text":"Range: ProtocolCategoryEnum
Required: True
name: protocol_execution_category\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_execution_category\ndomain_of:\n- ProtocolExecution\nrange: ProtocolCategoryEnum\nrequired: true\n\nThis property links a database object to the set of protocol executions within it.
URI: nmdc:protocol_execution_set
"},{"location":"protocol_execution_set/#inheritance","title":"Inheritance","text":"Range: ProtocolExecution
Multivalued: True
name: protocol_execution_set\ndescription: This property links a database object to the set of protocol executions\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: protocol_execution_set\ndomain_of:\n- Database\nrange: ProtocolExecution\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:protocol_link
"},{"location":"protocol_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MetabolomicsAnalysis no Study A study summarizes the overall goal of a research initiative and outlines the... yes ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no FiltrationProcess The process of segregation of phases; e no MetatranscriptomeAnnotation no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no CollectingBiosamplesFromSite no MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no LibraryPreparation no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"protocol_link/#properties","title":"Properties","text":"name: protocol_link\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: protocol_link\ndomain_of:\n- PlannedProcess\n- Study\nrange: Protocol\n\nSlot to store additional comments about laboratory or workflow output. For workflow output it may describe the particular workflow stage that failed. (ie Failed at call-stage due to a malformed fastq file).
URI: nmdc:qc_comment
"},{"location":"qc_comment/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MetabolomicsAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no FiltrationProcess The process of segregation of phases; e no MetatranscriptomeAnnotation no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no CollectingBiosamplesFromSite no MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no LibraryPreparation no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"qc_comment/#properties","title":"Properties","text":"name: qc_comment\ndescription: Slot to store additional comments about laboratory or workflow output.\n For workflow output it may describe the particular workflow stage that failed. (ie\n Failed at call-stage due to a malformed fastq file).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_comment\ndomain_of:\n- PlannedProcess\nrange: string\n\nProvides a summary about what caused a lab or workflow process to fail
URI: nmdc:qc_failure_what
"},{"location":"qc_failure_what/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FailureCategorization no"},{"location":"qc_failure_what/#properties","title":"Properties","text":"name: qc_failure_what\ndescription: Provides a summary about what caused a lab or workflow process to fail\ncomments:\n- For example, low read count from a sequencer, malformed fastq files, etc.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_failure_what\ndomain_of:\n- FailureCategorization\nrange: FailureWhatEnum\n\nDescribes the nmdc schema class that corresonds to where the failure occurred. Most commonly this would be the same as Class that generated the results.
URI: nmdc:qc_failure_where
"},{"location":"qc_failure_where/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FailureCategorization no"},{"location":"qc_failure_where/#properties","title":"Properties","text":"name: qc_failure_where\ndescription: Describes the nmdc schema class that corresonds to where the failure\n occurred. Most commonly this would be the same as Class that generated the results.\ncomments:\n- If the assembly size was too small to proceed to annotation failure_where would\n be MetagenomeAssembly.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_failure_where\ndomain_of:\n- FailureCategorization\nrange: FailureWhereEnum\n\nStores information about the result of a process (ie the process of sequencing a library may have for qc_status of 'fail' if not enough data was generated)
URI: nmdc:qc_status
"},{"location":"qc_status/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MetabolomicsAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no FiltrationProcess The process of segregation of phases; e no MetatranscriptomeAnnotation no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no CollectingBiosamplesFromSite no MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no LibraryPreparation no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"qc_status/#properties","title":"Properties","text":"name: qc_status\ndescription: Stores information about the result of a process (ie the process of sequencing\n a library may have for qc_status of 'fail' if not enough data was generated)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: qc_status\ndomain_of:\n- PlannedProcess\nrange: StatusEnum\n\nThe quadrant position of the sampling room within the building
URI: MIXS:0000820
"},{"location":"quad_pos/#inheritance","title":"Inheritance","text":"name: quad_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The quadrant position of the sampling room within the building\ntitle: quadrant position\nexamples:\n- value: West side\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- quadrant position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000820\nalias: quad_pos\ndomain_of:\n- Biosample\nrange: quad_pos_enum\nmultivalued: false\n\nInformation about treatment involving exposure of plant or a plant part to a particular radiation regimen; should include the radiation type, amount or intensity administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple radiation regimens
URI: MIXS:0000575
"},{"location":"radiation_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: radiation_regm\nannotations:\n expected_value:\n tag: expected_value\n value: radiation type name;radiation amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: rad, gray\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving exposure of plant or a plant part\n to a particular radiation regimen; should include the radiation type, amount or\n intensity administered, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple radiation regimens\ntitle: radiation regimen\nexamples:\n- value: gamma radiation;60 gray;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- radiation regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000575\nalias: radiation_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nInformation about treatment involving an exposure to a given amount of rainfall, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000576
"},{"location":"rainfall_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: rainfall_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to a given amount of\n rainfall, treatment regimen including how many times the treatment was repeated,\n how long each treatment lasted, and the start and end time of the entire treatment;\n can include multiple regimens\ntitle: rainfall regimen\nexamples:\n- value: 15 millimeter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rainfall regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000576\nalias: rainfall_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nAnaerobic digesters can be designed and engineered to operate using a number of different process configurations, as batch or continuous, mesophilic, high solid or low solid, and single stage or multistage
URI: MIXS:0000350
"},{"location":"reactor_type/#inheritance","title":"Inheritance","text":"name: reactor_type\nannotations:\n expected_value:\n tag: expected_value\n value: reactor type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Anaerobic digesters can be designed and engineered to operate using a\n number of different process configurations, as batch or continuous, mesophilic,\n high solid or low solid, and single stage or multistage\ntitle: reactor type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reactor type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000350\nalias: reactor_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:read_qc_analysis_statistic
"},{"location":"read_qc_analysis_statistic/#inheritance","title":"Inheritance","text":"name: read_qc_analysis_statistic\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: read_qc_analysis_statistic\nrange: string\n\nRedox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential
URI: MIXS:0000182
"},{"location":"redox_potential/#inheritance","title":"Inheritance","text":"name: redox_potential\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millivolt\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Redox potential, measured relative to a hydrogen cell, indicating oxidation\n or reduction potential\ntitle: redox potential\nexamples:\n- value: 300 millivolt\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- redox potential\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000182\nalias: redox_potential\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nPartial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air
URI: MIXS:0000121
"},{"location":"rel_air_humidity/#inheritance","title":"Inheritance","text":"name: rel_air_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Partial vapor and air pressure, density of the vapor and air, or by the\n actual mass of the vapor and air\ntitle: relative air humidity\nexamples:\n- value: 80%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative air humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000121\nalias: rel_air_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe recorded outside relative humidity value at the time of sampling
URI: MIXS:0000188
"},{"location":"rel_humidity_out/#inheritance","title":"Inheritance","text":"name: rel_humidity_out\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded outside relative humidity value at the time of sampling\ntitle: outside relative humidity\nexamples:\n- value: 12 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- outside relative humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000188\nalias: rel_humidity_out\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe sampling location within the train car
URI: MIXS:0000821
"},{"location":"rel_samp_loc/#inheritance","title":"Inheritance","text":"name: rel_samp_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The sampling location within the train car\ntitle: relative sampling location\nexamples:\n- value: center of car\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- relative sampling location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000821\nalias: rel_samp_loc\ndomain_of:\n- Biosample\nrange: rel_samp_loc_enum\nmultivalued: false\n\nIdentifiers assigned to a thing that is similar to that which is represented in NMDC. Related identifier are not an identical match and may have some variation.
URI: nmdc:related_identifiers
"},{"location":"related_identifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... yes"},{"location":"related_identifiers/#properties","title":"Properties","text":"name: related_identifiers\ndescription: Identifiers assigned to a thing that is similar to that which is represented\n in NMDC. Related identifier are not an identical match and may have some variation.\ntitle: Related Identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: related_identifiers\ndomain_of:\n- Study\nrange: string\n\nURI: nmdc:relations
"},{"location":"relations/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalEntity An atom or molecule that can be represented with a chemical formula no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no OrthologyGroup A set of genes or gene products in which all members are orthologous no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no EnvironmentalMaterialTerm no OntologyClass A representation of class defined in an external ontology no"},{"location":"relations/#properties","title":"Properties","text":"Range: OntologyRelation
Multivalued: True
name: relations\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: relations\nowner: OntologyClass\ndomain_of:\n- OntologyClass\nrange: OntologyRelation\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nIf sending biological replicates, indicate the rep number here.
URI: nmdc:replicate_number
"},{"location":"replicate_number/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"replicate_number/#properties","title":"Properties","text":"Range: String
Recommended: True
name: replicate_number\ndescription: If sending biological replicates, indicate the rep number here.\ntitle: replicate number\ncomments:\n- This will guide staff in ensuring your samples are blocked & randomized correctly\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{integer}'\nalias: replicate_number\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nName of the reservoir (e.g. Carapebus)
URI: MIXS:0000303
"},{"location":"reservoir/#inheritance","title":"Inheritance","text":"name: reservoir\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the reservoir (e.g. Carapebus)\ntitle: reservoir name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- reservoir name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000303\nalias: reservoir\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000134
"},{"location":"resins_pc/#inheritance","title":"Inheritance","text":"name: resins_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: resins wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- resins wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000134\nalias: resins_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe relative resolution at which spectra were collected.
URI: nmdc:resolution_categories
"},{"location":"resolution_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no"},{"location":"resolution_categories/#properties","title":"Properties","text":"Range: ResolutionCategoryEnum
Multivalued: True
name: resolution_categories\ndescription: The relative resolution at which spectra were collected.\nexamples:\n- value: '[''high'', ''low'']'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: resolution_categories\ndomain_of:\n- MassSpectrometryConfiguration\nrange: ResolutionCategoryEnum\nmultivalued: true\n\n260/280 measurement of RNA sample purity
URI: nmdc:rna_absorb1
"},{"location":"rna_absorb1/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_absorb1/#properties","title":"Properties","text":"Range: Float
Recommended: True
name: rna_absorb1\ndescription: 260/280 measurement of RNA sample purity\ntitle: RNA absorbance 260/280\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 7\nstring_serialization: '{float}'\nalias: rna_absorb1\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\n260/230 measurement of RNA sample purity
URI: nmdc:rna_absorb2
"},{"location":"rna_absorb2/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_absorb2/#properties","title":"Properties","text":"Range: Float
Recommended: True
name: rna_absorb2\ndescription: 260/230 measurement of RNA sample purity\ntitle: RNA absorbance 260/230\ncomments:\n- Recommended value is between 1 and 3.\nexamples:\n- value: '2.02'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 8\nstring_serialization: '{float}'\nalias: rna_absorb2\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\n\nProvide information on the site your RNA sample was collected from
URI: nmdc:rna_collect_site
"},{"location":"rna_collect_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_collect_site/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_collect_site\ndescription: Provide information on the site your RNA sample was collected from\ntitle: RNA collection site\nexamples:\n- value: untreated pond water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 15\nstring_serialization: '{text}'\nalias: rna_collect_site\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_concentration
"},{"location":"rna_concentration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_concentration/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: rna_concentration\ntitle: RNA concentration in ng/ul\ncomments:\n- Units must be in ng/uL. Enter the numerical part only. Must be calculated using\n a fluorometric method. Acceptable values are 0-2000.\nexamples:\n- value: '100'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:nucleic_acid_concentration\nrank: 5\nstring_serialization: '{float}'\nalias: rna_concentration\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nTube or plate (96-well)
URI: nmdc:rna_cont_type
"},{"location":"rna_cont_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_type/#properties","title":"Properties","text":"Range: JgiContTypeEnum
Recommended: True
name: rna_cont_type\ndescription: Tube or plate (96-well)\ntitle: RNA container type\nexamples:\n- value: plate\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 10\nalias: rna_cont_type\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: JgiContTypeEnum\nrecommended: true\n\nURI: nmdc:rna_cont_well
"},{"location":"rna_cont_well/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_cont_well/#properties","title":"Properties","text":"Range: String
Recommended: True
Regex pattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$
name: rna_cont_well\ntitle: RNA plate position\ncomments:\n- Required when 'plate' is selected for container type.\n- Leave blank if the sample will be shipped in a tube.\n- JGI will not process samples in corner wells, so A1, A12, H1 and H12 will not pass\n validation.\n- For partial plates, fill by columns, like B1-G1,A2-H2,A3-D3 (NOT A2-A11,B1-B8).\nexamples:\n- value: B2\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 11\nstring_serialization: '{96 well plate pos}'\nalias: rna_cont_well\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\npattern: ^(?!A1$|A12$|H1$|H12$)(([A-H][1-9])|([A-H]1[0-2]))$\n\nURI: nmdc:rna_container_id
"},{"location":"rna_container_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_container_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_container_id\ntitle: RNA container label\ncomments:\n- Must be unique across all tubes and plates, and <20 characters. All samples in a\n plate should have the same plate label.\nexamples:\n- value: Pond_MT_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 9\nstring_serialization: '{text < 20 characters}'\nalias: rna_container_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nDescribe the method/protocol/kit used to extract DNA/RNA.
URI: nmdc:rna_isolate_meth
"},{"location":"rna_isolate_meth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_isolate_meth/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_isolate_meth\ndescription: Describe the method/protocol/kit used to extract DNA/RNA.\ntitle: RNA isolation method\nexamples:\n- value: phenol/chloroform extraction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Sample Isolation Method\nrank: 16\nstring_serialization: '{text}'\nalias: rna_isolate_meth\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nList any organisms known or suspected to grow in co-culture, as well as estimated % of the organism in that culture.
URI: nmdc:rna_organisms
"},{"location":"rna_organisms/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_organisms/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_organisms\ndescription: List any organisms known or suspected to grow in co-culture, as well\n as estimated % of the organism in that culture.\ntitle: RNA expected organisms\nexamples:\n- value: expected to contain microbes (59%) fungi (30%), viruses (10%), tadpoles (1%)\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 14\nstring_serialization: '{text}'\nalias: rna_organisms\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_project_contact
"},{"location":"rna_project_contact/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_project_contact/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_project_contact\ntitle: RNA seq project contact\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: John Jones\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 18\nstring_serialization: '{text}'\nalias: rna_project_contact\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_samp_id
"},{"location":"rna_samp_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_samp_id/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_samp_id\ntitle: RNA sample ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '187654'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{text}'\nalias: rna_samp_id\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nSolution in which the RNA sample has been suspended
URI: nmdc:rna_sample_format
"},{"location":"rna_sample_format/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_format/#properties","title":"Properties","text":"Range: RNASampleFormatEnum
Recommended: True
name: rna_sample_format\ndescription: Solution in which the RNA sample has been suspended\ntitle: RNA sample format\nexamples:\n- value: Water\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 12\nalias: rna_sample_format\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: RNASampleFormatEnum\nrecommended: true\n\nGive the RNA sample a name that is meaningful to you. Sample names must be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.
URI: nmdc:rna_sample_name
"},{"location":"rna_sample_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_sample_name/#properties","title":"Properties","text":"Range: String
Recommended: True
Minimum Value: 0
Maximum Value: 2000
name: rna_sample_name\ndescription: Give the RNA sample a name that is meaningful to you. Sample names must\n be unique across all JGI projects and contain a-z, A-Z, 0-9, - and _ only.\ntitle: RNA sample name\nexamples:\n- value: JGI_pond_041618\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 4\nstring_serialization: '{text}'\nalias: rna_sample_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\nminimum_value: 0\nmaximum_value: 2000\n\nURI: nmdc:rna_seq_project
"},{"location":"rna_seq_project/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project\ntitle: RNA seq project ID\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: '1191234'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Seq Project ID\nrank: 1\nstring_serialization: '{text}'\nalias: rna_seq_project\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_seq_project_name
"},{"location":"rna_seq_project_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_name/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project_name\ntitle: RNA seq project name\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: JGI Pond metatranscriptomics\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nstring_serialization: '{text}'\nalias: rna_seq_project_name\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_seq_project_pi
"},{"location":"rna_seq_project_pi/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_seq_project_pi/#properties","title":"Properties","text":"Range: String
Recommended: True
name: rna_seq_project_pi\ntitle: RNA seq project PI\ncomments:\n- Do not edit these values. A template will be provided by NMDC in which these values\n have been pre-filled.\nexamples:\n- value: Jane Johnson\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 17\nstring_serialization: '{text}'\nalias: rna_seq_project_pi\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: string\nrecommended: true\n\nURI: nmdc:rna_volume
"},{"location":"rna_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"rna_volume/#properties","title":"Properties","text":"Range: Float
Recommended: True
Minimum Value: 0
Maximum Value: 1000
name: rna_volume\ntitle: RNA volume in ul\ncomments:\n- Units must be in uL. Enter the numerical part only. Value must be 0-1000. This form\n accepts values < 25, but JGI may refuse to process them unless permission has been\n granted by a project manager\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 6\nstring_serialization: '{float}'\nalias: rna_volume\ndomain_of:\n- Biosample\nslot_group: JGI-Metatranscriptomics\nrange: float\nrecommended: true\nminimum_value: 0\nmaximum_value: 1000\n\nThe rate at which outside air replaces indoor air in a given space
URI: MIXS:0000169
"},{"location":"room_air_exch_rate/#inheritance","title":"Inheritance","text":"name: room_air_exch_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: liter per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The rate at which outside air replaces indoor air in a given space\ntitle: room air exchange rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room air exchange rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000169\nalias: room_air_exch_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe unique details and component parts that, together, form the architecture of a distinguisahable space within a built structure
URI: MIXS:0000233
"},{"location":"room_architec_elem/#inheritance","title":"Inheritance","text":"name: room_architec_elem\nannotations:\n expected_value:\n tag: expected_value\n value: free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The unique details and component parts that, together, form the architecture\n of a distinguisahable space within a built structure\ntitle: room architectural elements\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room architectural elements\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000233\nalias: room_architec_elem\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe condition of the room at the time of sampling
URI: MIXS:0000822
"},{"location":"room_condt/#inheritance","title":"Inheritance","text":"name: room_condt\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The condition of the room at the time of sampling\ntitle: room condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000822\nalias: room_condt\ndomain_of:\n- Biosample\nrange: room_condt_enum\nmultivalued: false\n\nList of rooms connected to the sampling room by a doorway
URI: MIXS:0000826
"},{"location":"room_connected/#inheritance","title":"Inheritance","text":"name: room_connected\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of rooms connected to the sampling room by a doorway\ntitle: rooms connected by a doorway\nexamples:\n- value: office\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms connected by a doorway\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000826\nalias: room_connected\ndomain_of:\n- Biosample\nrange: room_connected_enum\nmultivalued: false\n\nThe total count of rooms in the built structure including all room types
URI: MIXS:0000234
"},{"location":"room_count/#inheritance","title":"Inheritance","text":"name: room_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total count of rooms in the built structure including all room types\ntitle: room count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000234\nalias: room_count\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe length, width and height of sampling room
URI: MIXS:0000192
"},{"location":"room_dim/#inheritance","title":"Inheritance","text":"name: room_dim\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The length, width and height of sampling room\ntitle: room dimensions\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room dimensions\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit} x {integer} {unit} x {integer} {unit}'\nslot_uri: MIXS:0000192\nalias: room_dim\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDistance between doors (meters) in the hallway between the sampling room and adjacent rooms
URI: MIXS:0000193
"},{"location":"room_door_dist/#inheritance","title":"Inheritance","text":"name: room_door_dist\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Distance between doors (meters) in the hallway between the sampling room\n and adjacent rooms\ntitle: room door distance\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room door distance\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000193\nalias: room_door_dist\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of room(s) (room number, room name) sharing a door with the sampling room
URI: MIXS:0000242
"},{"location":"room_door_share/#inheritance","title":"Inheritance","text":"name: room_door_share\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) sharing a door with the sampling\n room\ntitle: rooms that share a door with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a door with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000242\nalias: room_door_share\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of room(s) (room number, room name) located in the same hallway as sampling room
URI: MIXS:0000238
"},{"location":"room_hallway/#inheritance","title":"Inheritance","text":"name: room_hallway\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) located in the same hallway\n as sampling room\ntitle: rooms that are on the same hallway\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that are on the same hallway\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000238\nalias: room_hallway\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe position of the room within the building
URI: MIXS:0000823
"},{"location":"room_loc/#inheritance","title":"Inheritance","text":"name: room_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The position of the room within the building\ntitle: room location in building\nexamples:\n- value: interior room\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room location in building\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000823\nalias: room_loc\ndomain_of:\n- Biosample\nrange: room_loc_enum\nmultivalued: false\n\nThe history of moisture damage or mold in the past 12 months. Number of events of moisture damage or mold observed
URI: MIXS:0000235
"},{"location":"room_moist_dam_hist/#inheritance","title":"Inheritance","text":"name: room_moist_dam_hist\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The history of moisture damage or mold in the past 12 months. Number\n of events of moisture damage or mold observed\ntitle: room moisture damage or mold history\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room moisture damage or mold history\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000235\nalias: room_moist_dam_hist\ndomain_of:\n- Biosample\nrange: integer\nmultivalued: false\n\nThe net floor area of sampling room. Net area excludes wall thicknesses
URI: MIXS:0000194
"},{"location":"room_net_area/#inheritance","title":"Inheritance","text":"name: room_net_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square feet, square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The net floor area of sampling room. Net area excludes wall thicknesses\ntitle: room net area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room net area\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000194\nalias: room_net_area\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nCount of room occupancy at time of sampling
URI: MIXS:0000236
"},{"location":"room_occup/#inheritance","title":"Inheritance","text":"name: room_occup\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Count of room occupancy at time of sampling\ntitle: room occupancy\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room occupancy\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000236\nalias: room_occup\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe horizontal sampling position in the room relative to architectural elements
URI: MIXS:0000824
"},{"location":"room_samp_pos/#inheritance","title":"Inheritance","text":"name: room_samp_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The horizontal sampling position in the room relative to architectural\n elements\ntitle: room sampling position\nexamples:\n- value: south corner\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room sampling position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000824\nalias: room_samp_pos\ndomain_of:\n- Biosample\nrange: room_samp_pos_enum\nmultivalued: false\n\nThe main purpose or activity of the sampling room. A room is any distinguishable space within a structure
URI: MIXS:0000825
"},{"location":"room_type/#inheritance","title":"Inheritance","text":"name: room_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The main purpose or activity of the sampling room. A room is any distinguishable\n space within a structure\ntitle: room type\nexamples:\n- value: bathroom\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000825\nalias: room_type\ndomain_of:\n- Biosample\nrange: room_type_enum\nmultivalued: false\n\nVolume of sampling room
URI: MIXS:0000195
"},{"location":"room_vol/#inheritance","title":"Inheritance","text":"name: room_vol\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic feet, cubic meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Volume of sampling room\ntitle: room volume\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room volume\nrank: 1000\nis_a: core field\nstring_serialization: '{integer} {unit}'\nslot_uri: MIXS:0000195\nalias: room_vol\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nList of room(s) (room number, room name) sharing a wall with the sampling room
URI: MIXS:0000243
"},{"location":"room_wall_share/#inheritance","title":"Inheritance","text":"name: room_wall_share\nannotations:\n expected_value:\n tag: expected_value\n value: room name;room number\n occurrence:\n tag: occurrence\n value: '1'\ndescription: List of room(s) (room number, room name) sharing a wall with the sampling\n room\ntitle: rooms that share a wall with sampling room\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooms that share a wall with sampling room\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{integer}'\nslot_uri: MIXS:0000243\nalias: room_wall_share\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nNumber of windows in the room
URI: MIXS:0000237
"},{"location":"room_window_count/#inheritance","title":"Inheritance","text":"name: room_window_count\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Number of windows in the room\ntitle: room window count\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- room window count\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000237\nalias: room_window_count\ndomain_of:\n- Biosample\nrange: integer\nmultivalued: false\n\nRelevant rooting conditions such as field plot size, sowing density, container dimensions, number of plants per container.
URI: MIXS:0001061
"},{"location":"root_cond/#inheritance","title":"Inheritance","text":"name: root_cond\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Relevant rooting conditions such as field plot size, sowing density,\n container dimensions, number of plants per container.\ntitle: rooting conditions\nexamples:\n- value: http://himedialabs.com/TD/PT158.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001061\nalias: root_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSource of organic carbon in the culture rooting medium; e.g. sucrose.
URI: MIXS:0000577
"},{"location":"root_med_carbon/#inheritance","title":"Inheritance","text":"name: root_med_carbon\nannotations:\n expected_value:\n tag: expected_value\n value: carbon source name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Source of organic carbon in the culture rooting medium; e.g. sucrose.\ntitle: rooting medium carbon\nexamples:\n- value: sucrose\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium carbon\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000577\nalias: root_med_carbon\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMeasurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).
URI: MIXS:0000578
"},{"location":"root_med_macronutr/#inheritance","title":"Inheritance","text":"name: root_med_macronutr\nannotations:\n expected_value:\n tag: expected_value\n value: macronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of the culture rooting medium macronutrients (N,P, K, Ca,\n Mg, S); e.g. KH2PO4 (170\u00ac\u2020mg/L).\ntitle: rooting medium macronutrients\nexamples:\n- value: KH2PO4;170\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium macronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000578\nalias: root_med_macronutr\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nMeasurement of the culture rooting medium micronutrients (Fe, Mn, Zn, B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).
URI: MIXS:0000579
"},{"location":"root_med_micronutr/#inheritance","title":"Inheritance","text":"name: root_med_micronutr\nannotations:\n expected_value:\n tag: expected_value\n value: micronutrient name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of the culture rooting medium micronutrients (Fe, Mn, Zn,\n B, Cu, Mo); e.g. H3BO3 (6.2\u00ac\u2020mg/L).\ntitle: rooting medium micronutrients\nexamples:\n- value: H3BO3;6.2\u00ac\u2020milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium micronutrients\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000579\nalias: root_med_micronutr\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\npH measurement of the culture rooting medium; e.g. 5.5.
URI: MIXS:0001062
"},{"location":"root_med_ph/#inheritance","title":"Inheritance","text":"name: root_med_ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: pH measurement of the culture rooting medium; e.g. 5.5.\ntitle: rooting medium pH\nexamples:\n- value: '7.5'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001062\nalias: root_med_ph\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nGrowth regulators in the culture rooting medium such as cytokinins, auxins, gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.
URI: MIXS:0000581
"},{"location":"root_med_regl/#inheritance","title":"Inheritance","text":"name: root_med_regl\nannotations:\n expected_value:\n tag: expected_value\n value: regulator name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Growth regulators in the culture rooting medium such as cytokinins, auxins,\n gybberellins, abscisic acid; e.g. 0.5\u00ac\u2020mg/L NAA.\ntitle: rooting medium regulators\nexamples:\n- value: abscisic acid;0.75 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium regulators\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000581\nalias: root_med_regl\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSpecification of the solidifying agent in the culture rooting medium; e.g. agar.
URI: MIXS:0001063
"},{"location":"root_med_solid/#inheritance","title":"Inheritance","text":"name: root_med_solid\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specification of the solidifying agent in the culture rooting medium;\n e.g. agar.\ntitle: rooting medium solidifier\nexamples:\n- value: agar\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium solidifier\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001063\nalias: root_med_solid\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nOrganic supplements of the culture rooting medium, such as vitamins, amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid (0.5\u00ac\u2020mg/L).
URI: MIXS:0000580
"},{"location":"root_med_suppl/#inheritance","title":"Inheritance","text":"name: root_med_suppl\nannotations:\n expected_value:\n tag: expected_value\n value: supplement name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Organic supplements of the culture rooting medium, such as vitamins,\n amino acids, organic acids, antibiotics activated charcoal; e.g. nicotinic acid\n (0.5\u00ac\u2020mg/L).\ntitle: rooting medium organic supplements\nexamples:\n- value: nicotinic acid;0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- rooting medium organic supplements\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000580\nalias: root_med_suppl\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe total concentration of all dissolved salts in a liquid or solid sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater.
URI: MIXS:0000183
"},{"location":"salinity/#inheritance","title":"Inheritance","text":"name: salinity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: practical salinity unit, percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total concentration of all dissolved salts in a liquid or solid sample.\n While salinity can be measured by a complete chemical analysis, this method is difficult\n and time consuming. More often, it is instead derived from the conductivity measurement.\n This is known as practical salinity. These derivations compare the specific conductance\n of the sample to a salinity standard such as seawater.\ntitle: salinity\nexamples:\n- value: 25 practical salinity unit\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000183\nalias: salinity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCategorical description of the sample's salinity. Examples: halophile, halotolerant, hypersaline, huryhaline
URI: nmdc:salinity_category
"},{"location":"salinity_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"salinity_category/#properties","title":"Properties","text":"name: salinity_category\ndescription: 'Categorical description of the sample''s salinity. Examples: halophile,\n halotolerant, hypersaline, huryhaline'\nnotes:\n- maps to gold:salinity\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-metadata/pull/297\nrank: 1000\nalias: salinity_category\ndomain_of:\n- Biosample\nrange: string\n\nReference or method used in determining salinity
URI: MIXS:0000341
"},{"location":"salinity_meth/#inheritance","title":"Inheritance","text":"name: salinity_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining salinity\ntitle: salinity method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salinity method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000341\nalias: salinity_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about treatment involving use of salts as supplement to liquid and soil growth media; should include the name of salt, amount administered, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple salt regimens
URI: MIXS:0000582
"},{"location":"salt_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: salt_regm\nannotations:\n expected_value:\n tag: expected_value\n value: salt name;salt amount;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving use of salts as supplement to liquid\n and soil growth media; should include the name of salt, amount administered, treatment\n regimen including how many times the treatment was repeated, how long each treatment\n lasted, and the start and end time of the entire treatment; can include multiple\n salt regimens\ntitle: salt regimen\nexamples:\n- value: NaCl;5 gram per liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- salt regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000582\nalias: salt_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nReason for the sample
URI: MIXS:0000860
"},{"location":"samp_capt_status/#inheritance","title":"Inheritance","text":"name: samp_capt_status\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reason for the sample\ntitle: sample capture status\nexamples:\n- value: farm sample\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample capture status\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000860\nalias: samp_capt_status\ndomain_of:\n- Biosample\nrange: samp_capt_status_enum\nmultivalued: false\n\nThe device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
URI: MIXS:0000002
"},{"location":"samp_collec_device/#inheritance","title":"Inheritance","text":"name: samp_collec_device\nannotations:\n expected_value:\n tag: expected_value\n value: device name\ndescription: The device used to collect an environmental sample. This field accepts\n terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).\n This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).\ntitle: sample collection device\nexamples:\n- value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection device\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000002\nalias: samp_collec_device\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe method employed for collecting the sample.
URI: MIXS:0001225
"},{"location":"samp_collec_method/#inheritance","title":"Inheritance","text":"name: samp_collec_method\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url , or text\ndescription: The method employed for collecting the sample.\ntitle: sample collection method\nexamples:\n- value: swabbing\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection method\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001225\nalias: samp_collec_method\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nSampling point on the asset were sample was collected (e.g. Wellhead, storage tank, separator, etc). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0001015
"},{"location":"samp_collect_point/#inheritance","title":"Inheritance","text":"name: samp_collect_point\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sampling point on the asset were sample was collected (e.g. Wellhead,\n storage tank, separator, etc). If \"other\" is specified, please propose entry in\n \"additional info\" field\ntitle: sample collection point\nexamples:\n- value: well\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample collection point\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001015\nalias: samp_collect_point\ndomain_of:\n- Biosample\nrange: samp_collect_point_enum\nmultivalued: false\n\nStage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen.
URI: MIXS:0000249
"},{"location":"samp_dis_stage/#inheritance","title":"Inheritance","text":"name: samp_dis_stage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Stage of the disease at the time of sample collection, e.g. inoculation,\n penetration, infection, growth and reproduction, dissemination of pathogen.\ntitle: sample disease stage\nexamples:\n- value: infection\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample disease stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000249\nalias: samp_dis_stage\ndomain_of:\n- Biosample\nrange: samp_dis_stage_enum\nmultivalued: false\n\nThe floor of the building, where the sampling room is located
URI: MIXS:0000828
"},{"location":"samp_floor/#inheritance","title":"Inheritance","text":"name: samp_floor\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The floor of the building, where the sampling room is located\ntitle: sampling floor\nexamples:\n- value: 4th floor\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling floor\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000828\nalias: samp_floor\ndomain_of:\n- Biosample\nrange: samp_floor_enum\nmultivalued: false\n\nMetal corrosion rate is the speed of metal deterioration due to environmental conditions. As environmental conditions change corrosion rates change accordingly. Therefore, long term corrosion rates are generally more informative than short term rates and for that reason they are preferred during reporting. In the case of suspected MIC, corrosion rate measurements at the time of sampling might provide insights into the involvement of certain microbial community members in MIC as well as potential microbial interplays
URI: MIXS:0000136
"},{"location":"samp_loc_corr_rate/#inheritance","title":"Inheritance","text":"name: samp_loc_corr_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value range\n preferred_unit:\n tag: preferred_unit\n value: millimeter per year\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Metal corrosion rate is the speed of metal deterioration due to environmental\n conditions. As environmental conditions change corrosion rates change accordingly.\n Therefore, long term corrosion rates are generally more informative than short term\n rates and for that reason they are preferred during reporting. In the case of suspected\n MIC, corrosion rate measurements at the time of sampling might provide insights\n into the involvement of certain microbial community members in MIC as well as potential\n microbial interplays\ntitle: corrosion rate at sample location\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- corrosion rate at sample location\nrank: 1000\nis_a: core field\nstring_serialization: '{float} - {float} {unit}'\nslot_uri: MIXS:0000136\nalias: samp_loc_corr_rate\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.
URI: MIXS:0000016
"},{"location":"samp_mat_process/#inheritance","title":"Inheritance","text":"name: samp_mat_process\nannotations:\n expected_value:\n tag: expected_value\n value: text\ndescription: A brief description of any processing applied to the sample during or\n after retrieving the sample from environment, or a link to the relevant protocol(s)\n performed.\ntitle: sample material processing\nexamples:\n- value: filtering of seawater, storing samples in ethanol\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample material processing\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000016\nalias: samp_mat_process\ndomain_of:\n- Biosample\nrange: ControlledTermValue\nmultivalued: false\n\nIn non deviated well, measured depth is equal to the true vertical depth, TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the MD is the length of trajectory of the borehole measured from the same reference or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000413
"},{"location":"samp_md/#inheritance","title":"Inheritance","text":"name: samp_md\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;enumeration\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: In non deviated well, measured depth is equal to the true vertical depth,\n TVD (TVD=TVDSS plus the reference or datum it refers to). In deviated wells, the\n MD is the length of trajectory of the borehole measured from the same reference\n or datum. Common datums used are ground level (GL), drilling rig floor (DF), rotary\n table (RT), kelly bushing (KB) and mean sea level (MSL). If \"other\" is specified,\n please propose entry in \"additional info\" field\ntitle: sample measured depth\nexamples:\n- value: 1534 meter;MSL\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample measured depth\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000413\nalias: samp_md\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nA local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. Use of a globally unique identifier for the field source_mat_id is recommended in addition to sample_name.
URI: MIXS:0001107
"},{"location":"samp_name/#inheritance","title":"Inheritance","text":"name: samp_name\nannotations:\n expected_value:\n tag: expected_value\n value: text\ndescription: A local identifier or name that for the material sample used for extracting\n nucleic acids, and subsequent sequencing. It can refer either to the original material\n collected or to any derived sub-samples. It can have any format, but we suggest\n that you make it concise, unique and consistent within your lab, and as informative\n as possible. INSDC requires every sample name from a single Submitter to be unique.\n Use of a globally unique identifier for the field source_mat_id is recommended in\n addition to sample_name.\ntitle: sample name\nexamples:\n- value: ISDsoil1\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample name\nrank: 1000\nis_a: investigation field\nstring_serialization: '{text}'\nslot_uri: MIXS:0001107\nalias: samp_name\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nPreservative added to the sample (e.g. Rnalater, alcohol, formaldehyde, etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)
URI: MIXS:0000463
"},{"location":"samp_preserv/#inheritance","title":"Inheritance","text":"name: samp_preserv\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: milliliter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Preservative added to the sample (e.g. Rnalater, alcohol, formaldehyde,\n etc.). Where appropriate include volume added (e.g. Rnalater; 2 ml)\ntitle: preservative added to sample\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- preservative added to sample\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000463\nalias: samp_preserv\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSampling room number. This ID should be consistent with the designations on the building floor plans
URI: MIXS:0000244
"},{"location":"samp_room_id/#inheritance","title":"Inheritance","text":"name: samp_room_id\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sampling room number. This ID should be consistent with the designations\n on the building floor plans\ntitle: sampling room ID or name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling room ID or name\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000244\nalias: samp_room_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.
URI: MIXS:0000001
"},{"location":"samp_size/#inheritance","title":"Inheritance","text":"name: samp_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, liter\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n collected.\ntitle: amount or size of sample collected\nexamples:\n- value: 5 liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- amount or size of sample collected\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000001\nalias: samp_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMethod by which samples are sorted; open face filter collecting total suspended particles, prefilter to remove particles larger than X micrometers in diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade impactor.
URI: MIXS:0000216
"},{"location":"samp_sort_meth/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: samp_sort_meth\nannotations:\n expected_value:\n tag: expected_value\n value: description of method\n occurrence:\n tag: occurrence\n value: m\ndescription: Method by which samples are sorted; open face filter collecting total\n suspended particles, prefilter to remove particles larger than X micrometers in\n diameter, where common values of X would be 10 and 2.5 full size sorting in a cascade\n impactor.\ntitle: sample size sorting method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample size sorting method\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000216\nalias: samp_sort_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nDuration for which the sample was stored
URI: MIXS:0000116
"},{"location":"samp_store_dur/#inheritance","title":"Inheritance","text":"name: samp_store_dur\nannotations:\n expected_value:\n tag: expected_value\n value: duration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Duration for which the sample was stored\ntitle: sample storage duration\nexamples:\n- value: P1Y6M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage duration\nrank: 1000\nis_a: core field\nstring_serialization: '{duration}'\nslot_uri: MIXS:0000116\nalias: samp_store_dur\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nLocation at which sample was stored, usually name of a specific freezer/room
URI: MIXS:0000755
"},{"location":"samp_store_loc/#inheritance","title":"Inheritance","text":"name: samp_store_loc\nannotations:\n expected_value:\n tag: expected_value\n value: location name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Location at which sample was stored, usually name of a specific freezer/room\ntitle: sample storage location\nexamples:\n- value: Freezer no:5\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage location\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000755\nalias: samp_store_loc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nTemperature at which sample was stored, e.g. -80 degree Celsius
URI: MIXS:0000110
"},{"location":"samp_store_temp/#inheritance","title":"Inheritance","text":"name: samp_store_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature at which sample was stored, e.g. -80 degree Celsius\ntitle: sample storage temperature\nexamples:\n- value: -80 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample storage temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000110\nalias: samp_store_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nName of sample sub-type. For example if \"sample type\" is \"Produced Water\" then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000999
"},{"location":"samp_subtype/#inheritance","title":"Inheritance","text":"name: samp_subtype\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of sample sub-type. For example if \"sample type\" is \"Produced Water\"\n then subtype could be \"Oil Phase\" or \"Water Phase\". If \"other\" is specified, please\n propose entry in \"additional info\" field\ntitle: sample subtype\nexamples:\n- value: biofilm\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample subtype\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000999\nalias: samp_subtype\ndomain_of:\n- Biosample\nrange: samp_subtype_enum\nmultivalued: false\n\nNCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample' for negative controls.
URI: MIXS:0001320
"},{"location":"samp_taxon_id/#inheritance","title":"Inheritance","text":"name: samp_taxon_id\nannotations:\n expected_value:\n tag: expected_value\n value: Taxonomy ID\ndescription: NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample.\n Use 'synthetic metagenome\u2019 for mock community/positive controls, or 'blank sample'\n for negative controls.\ntitle: Taxonomy ID of DNA sample\ncomments:\n- coal metagenome [NCBITaxon:1260732] would be a reasonable has_raw_value\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- Taxonomy ID of DNA sample\nrank: 1000\nis_a: investigation field\nslot_uri: MIXS:0001320\nalias: samp_taxon_id\ndomain_of:\n- Biosample\nrange: ControlledIdentifiedTermValue\nmultivalued: false\n\nThe recent and long term history of outside sampling
URI: MIXS:0000196
"},{"location":"samp_time_out/#inheritance","title":"Inheritance","text":"name: samp_time_out\nannotations:\n expected_value:\n tag: expected_value\n value: time\n preferred_unit:\n tag: preferred_unit\n value: hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recent and long term history of outside sampling\ntitle: sampling time outside\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling time outside\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000196\nalias: samp_time_out\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSample transport duration (in days or hrs) and temperature the sample was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)
URI: MIXS:0000410
"},{"location":"samp_transport_cond/#inheritance","title":"Inheritance","text":"name: samp_transport_cond\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: days;degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sample transport duration (in days or hrs) and temperature the sample\n was exposed to (e.g. 5.5 days; 20 \u00ac\u221eC)\ntitle: sample transport conditions\nexamples:\n- value: 5 days;-20 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample transport conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000410\nalias: samp_transport_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDepth of the sample i.e. The vertical distance between the sea level and the sampled position in the subsurface. Depth can be reported as an interval for subsurface samples e.g. 1325.75-1362.25 m
URI: MIXS:0000409
"},{"location":"samp_tvdss/#inheritance","title":"Inheritance","text":"name: samp_tvdss\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value or measurement value range\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Depth of the sample i.e. The vertical distance between the sea level\n and the sampled position in the subsurface. Depth can be reported as an interval\n for subsurface samples e.g. 1325.75-1362.25 m\ntitle: sample true vertical depth subsea\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample true vertical depth subsea\nrank: 1000\nis_a: core field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000409\nalias: samp_tvdss\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe type of material from which the sample was obtained. For the Hydrocarbon package, samples include types like core, rock trimmings, drill cuttings, piping section, coupon, pigging debris, solid deposit, produced fluid, produced water, injected water, swabs, etc. For the Food Package, samples are usually categorized as food, body products or tissues, or environmental material. This field accepts terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).
URI: MIXS:0000998
"},{"location":"samp_type/#inheritance","title":"Inheritance","text":"name: samp_type\nannotations:\n expected_value:\n tag: expected_value\n value: GENEPIO:0001246\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material from which the sample was obtained. For the Hydrocarbon\n package, samples include types like core, rock trimmings, drill cuttings, piping\n section, coupon, pigging debris, solid deposit, produced fluid, produced water,\n injected water, swabs, etc. For the Food Package, samples are usually categorized\n as food, body products or tissues, or environmental material. This field accepts\n terms listed under environmental specimen (http://purl.obolibrary.org/obo/GENEPIO_0001246).\ntitle: sample type\nexamples:\n- value: built environment sample [GENEPIO:0001248]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000998\nalias: samp_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nVolume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).
URI: MIXS:0000111
"},{"location":"samp_vol_we_dna_ext/#inheritance","title":"Inheritance","text":"name: samp_vol_we_dna_ext\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millliter, gram, milligram, square centimeter\ndescription: 'Volume (ml) or mass (g) of total collected sample processed for DNA\n extraction. Note: total sample collected should be entered under the term Sample\n Size (MIXS:0000001).'\ntitle: sample volume or weight for DNA extraction\nexamples:\n- value: 1500 milliliter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample volume or weight for DNA extraction\nrank: 1000\nis_a: nucleic acid sequence source field\nslot_uri: MIXS:0000111\nalias: samp_vol_we_dna_ext\nrange: QuantityValue\nmultivalued: false\n\nThe weather on the sampling day
URI: MIXS:0000827
"},{"location":"samp_weather/#inheritance","title":"Inheritance","text":"name: samp_weather\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The weather on the sampling day\ntitle: sampling day weather\nexamples:\n- value: foggy\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sampling day weather\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000827\nalias: samp_weather\ndomain_of:\n- Biosample\nrange: samp_weather_enum\nmultivalued: false\n\nName of the well (e.g. BXA1123) where sample was taken
URI: MIXS:0000296
"},{"location":"samp_well_name/#inheritance","title":"Inheritance","text":"name: samp_well_name\nannotations:\n expected_value:\n tag: expected_value\n value: name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Name of the well (e.g. BXA1123) where sample was taken\ntitle: sample well name\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sample well name\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000296\nalias: samp_well_name\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:sample_collection_day
"},{"location":"sample_collection_day/#properties","title":"Properties","text":"name: sample_collection_day\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_day\nrange: integer\n\nURI: nmdc:sample_collection_hour
"},{"location":"sample_collection_hour/#properties","title":"Properties","text":"name: sample_collection_hour\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_hour\nrange: integer\n\nURI: nmdc:sample_collection_minute
"},{"location":"sample_collection_minute/#properties","title":"Properties","text":"name: sample_collection_minute\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_minute\nrange: integer\n\nURI: nmdc:sample_collection_month
"},{"location":"sample_collection_month/#properties","title":"Properties","text":"name: sample_collection_month\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_month\nrange: string\n\nURI: nmdc:sample_collection_site
"},{"location":"sample_collection_site/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_collection_site/#properties","title":"Properties","text":"name: sample_collection_site\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_site\ndomain_of:\n- Biosample\nrange: string\n\nURI: nmdc:sample_collection_year
"},{"location":"sample_collection_year/#properties","title":"Properties","text":"name: sample_collection_year\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_collection_year\nrange: integer\n\nA unique identifier to assign parent-child, subsample, or sibling samples. This is relevant when a sample or other material was used to generate the new sample.
URI: nmdc:sample_link
"},{"location":"sample_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_link/#properties","title":"Properties","text":"Range: String
Multivalued: True
Recommended: True
name: sample_link\ndescription: A unique identifier to assign parent-child, subsample, or sibling samples.\n This is relevant when a sample or other material was used to generate the new sample.\ntitle: sample linkage\ncomments:\n- 'This field allows multiple entries separated by ; (Examples: Soil collected from\n the field will link with the soil used in an incubation. The soil a plant was grown\n in links to the plant sample. An original culture sample was transferred to a new\n vial and generated a new sample)'\nexamples:\n- value: IGSN:DSJ0284\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{text}:{text}'\nalias: sample_link\ndomain_of:\n- Biosample\nslot_group: Sample ID\nrange: string\nrecommended: true\nmultivalued: true\n\nThe total amount or size (volume (ml), mass (g) or area (m2) ) of sample sent to EMSL.
URI: nmdc:sample_shipped
"},{"location":"sample_shipped/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_shipped/#properties","title":"Properties","text":"Range: String
Recommended: True
name: sample_shipped\ndescription: The total amount or size (volume (ml), mass (g) or area (m2) ) of sample\n sent to EMSL.\ntitle: sample shipped amount\ncomments:\n- This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\nexamples:\n- value: 15 g\n- value: 100 uL\n- value: 5 mL\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 3\nstring_serialization: '{float} {unit}'\nalias: sample_shipped\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nThe chemical phase of a pure sample, or the state of a mixed sample
URI: nmdc:sample_state_information
"},{"location":"sample_state_information/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"sample_state_information/#properties","title":"Properties","text":"name: sample_state_information\ndescription: The chemical phase of a pure sample, or the state of a mixed sample\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sample_state_information\ndomain_of:\n- PortionOfSubstance\nrange: SampleStateEnum\n\nType of sample being submitted
URI: nmdc:sample_type
"},{"location":"sample_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"sample_type/#properties","title":"Properties","text":"Range: SampleTypeEnum
Recommended: True
name: sample_type\ndescription: Type of sample being submitted\ntitle: sample type\ncomments:\n- This can vary from 'environmental package' if the sample is an extraction.\nexamples:\n- value: water extracted soil\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 2\nalias: sample_type\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: SampleTypeEnum\nrecommended: true\n\nThe portion of the sample that is taken for downstream activity.
URI: nmdc:sampled_portion
"},{"location":"sampled_portion/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no"},{"location":"sampled_portion/#properties","title":"Properties","text":"Range: SamplePortionEnum
Multivalued: True
name: sampled_portion\ndescription: The portion of the sample that is taken for downstream activity.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: sampled_portion\ndomain_of:\n- SubSamplingProcess\nrange: SamplePortionEnum\nmultivalued: true\n\nSaturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity. There are three main methods to obtain SARA results. The most popular one is known as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)
URI: MIXS:0000131
"},{"location":"saturates_pc/#inheritance","title":"Inheritance","text":"name: saturates_pc\nannotations:\n expected_value:\n tag: expected_value\n value: name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Saturate, Aromatic, Resin and Asphaltene\u00ac\u2020(SARA) is an analysis method\n that divides\u00ac\u2020crude oil\u00ac\u2020components according to their polarizability and polarity.\n There are three main methods to obtain SARA results. The most popular one is known\n as the Iatroscan TLC-FID and is referred to as IP-143 (source: https://en.wikipedia.org/wiki/Saturate,_aromatic,_resin_and_asphaltene)'\ntitle: saturates wt%\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- saturates wt%\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000131\nalias: saturates_pc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nTotal size in bp of all scaffolds.
URI: nmdc:scaf_bp
"},{"location":"scaf_bp/#inheritance","title":"Inheritance","text":"name: scaf_bp\ndescription: Total size in bp of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_bp\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, the L50 is defined as the sequence length of the shortest scaffold at 50% of the total genome length.
URI: nmdc:scaf_l50
"},{"location":"scaf_l50/#inheritance","title":"Inheritance","text":"name: scaf_l50\ndescription: Given a set of scaffolds, the L50 is defined as the sequence length of\n the shortest scaffold at 50% of the total genome length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe L90 statistic is less than or equal to the L50 statistic; it is the length for which the collection of all scaffolds of that length or longer contains at least 90% of the sum of the lengths of all scaffolds.
URI: nmdc:scaf_l90
"},{"location":"scaf_l90/#inheritance","title":"Inheritance","text":"name: scaf_l90\ndescription: The L90 statistic is less than or equal to the L50 statistic; it is the\n length for which the collection of all scaffolds of that length or longer contains\n at least 90% of the sum of the lengths of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal size in bp of all scaffolds greater than 50 KB.
URI: nmdc:scaf_l_gt50k
"},{"location":"scaf_l_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_l_gt50k\ndescription: Total size in bp of all scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_l_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe sum of the (length*log(length)) of all scaffolds, times some constant. Increase the contiguity, the score will increase
URI: nmdc:scaf_logsum
"},{"location":"scaf_logsum/#inheritance","title":"Inheritance","text":"name: scaf_logsum\ndescription: The sum of the (length*log(length)) of all scaffolds, times some constant. Increase\n the contiguity, the score will increase\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_logsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nMaximum scaffold length.
URI: nmdc:scaf_max
"},{"location":"scaf_max/#inheritance","title":"Inheritance","text":"name: scaf_max\ndescription: Maximum scaffold length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_max\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, each with its own length, the N50 count is defined as the smallest number of scaffolds whose length sum makes up half of genome size.
URI: nmdc:scaf_n50
"},{"location":"scaf_n50/#inheritance","title":"Inheritance","text":"name: scaf_n50\ndescription: Given a set of scaffolds, each with its own length, the N50 count is\n defined as the smallest number of scaffolds whose length sum makes up half of genome\n size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n50\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nGiven a set of scaffolds, each with its own length, the N90 count is defined as the smallest number of scaffolds whose length sum makes up 90% of genome size.
URI: nmdc:scaf_n90
"},{"location":"scaf_n90/#inheritance","title":"Inheritance","text":"name: scaf_n90\ndescription: Given a set of scaffolds, each with its own length, the N90 count is\n defined as the smallest number of scaffolds whose length sum makes up 90% of genome\n size.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n90\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence count of scaffolds greater than 50 KB.
URI: nmdc:scaf_n_gt50k
"},{"location":"scaf_n_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_n_gt50k\ndescription: Total sequence count of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_n_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence size percentage of scaffolds greater than 50 KB.
URI: nmdc:scaf_pct_gt50k
"},{"location":"scaf_pct_gt50k/#inheritance","title":"Inheritance","text":"name: scaf_pct_gt50k\ndescription: Total sequence size percentage of scaffolds greater than 50 KB.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_pct_gt50k\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nPowersum of all scaffolds is the same as logsum except that it uses the sum of (length*(length^P)) for some power P (default P=0.25).
URI: nmdc:scaf_powsum
"},{"location":"scaf_powsum/#inheritance","title":"Inheritance","text":"name: scaf_powsum\ndescription: Powersum of all scaffolds is the same as logsum except that it uses the\n sum of (length*(length^P)) for some power P (default P=0.25).\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaf_powsum\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nTotal sequence count of all scaffolds.
URI: nmdc:scaffolds
"},{"location":"scaffolds/#inheritance","title":"Inheritance","text":"name: scaffolds\ndescription: Total sequence count of all scaffolds.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: metagenome_assembly_parameter\nalias: scaffolds\ndomain_of:\n- MetagenomeAssembly\n- MetatranscriptomeAssembly\nrange: float\n\nThe nmdc-schema's preferred serializations are YAML, closely followed by JSONSchema. MongoDB is the database of choice for storing data. The nmdc-schema is designed to be a bridge between these formats.
The nmdc-schema Makefiles use the linkml-validate and linkml-run-examples CLIs for build-time validation of data file, both of which build upon JSON Schema validation. linkml-validate can even validate against TSV, as long as the schema classes that are instantiated can reasonably be expressed in a table. Programmers can learn more about the internals of these tools at https://linkml.io/linkml/data/validating-data.html
We can conceive of validating a data file at two levels
All tools, libraries, or scripts generating NMDC data SHOULD instantiate Python data classes from the nmdc-schema PyPI package. It is strongly discouraged to generate Python dicts or JSON by any method other than object instantiation, even using high-quality, standard JSON libraries. That practice may generate valid data files when first tested but is likely to degrade over time. That degradation can be difficult to debug.
Mike Farrah's yq is a system dependency for the nmdc-schema. It can be used to validate legacy YAML and JSON data. If malformed YAML or JSON is presented to linkml-validate, the error messages may not be as helpful as the messages from yq or some other syntactical validator.
Start by reflecting on whether your data may be ahead of what the schema can currently account for.
For 1, you can make PR on the schema yaml. If you aren't comfortable editing LinkML YAML, then you can get help from one of the schema developers. We recommend filing a new ticket explaining the issue. Please include your error messages.
For 2, we suggest taking a minimal example approach. linkml-validate is very good at identifying schema violations in small, syntactically valid data files. Debugging can be aided in pulling out single data instances and first verifying that they are syntactically valid YAML or JSON. If you don't want to use yq, then you could paste one instance into a website like https://jsonlint.com/. A common issue in multi-instance files is using incorrect syntax for grouping the instances into a YAML or JSON array. Using a small subsample of your data and an online linter as above can aide in debugging this.
It is expected that data producers or transformers take the upfront initiative to validate their data.
Currently, not all providers of information to NMDC provide JSON - for example, GOLD is provided as database dumps, and an ETL process transforms this into JSON. In the future, we would like to move towards a situation where all information is provided as JSON.
"},{"location":"schema_element_deprecation_guide/","title":"Deprecating NMDC Schema elements","text":"By deprecating, rather than deleting, schema elements in the NMDC model, we ensure backward compatibility, extend user trust, and provide a valuable historical record, aiding in the understanding of the model's evolution. Therefore, 'deleting' a schema element in NMDC is instead, a two-step (and two-release) deprecation process.
"},{"location":"schema_element_deprecation_guide/#first-release-cycle","title":"First release cycle:","text":"# doi_awards deprecated on 2023-11-12 in a class's usage). * note: If a replacement is not warranted, then using only the deprecated metadata tag with an explanation string and issue link is fine.
** note: For a deprecated class, references could be in the is_a or mixin elements of another class, or in the domain or range elements of an existing slot. For deprecated slots, check all classes that reference that slot, etc.
Please see LinkML SchemaView documentation for general information. It has several good examples of how to use this module in a python script or from the command line. https://linkml.io/linkml/developers/schemaview.html#schemaview
There are also several notebooks that demonstrate SchemaView usage in the LinkML-runtime repository: https://github.com/linkml/linkml-runtime/tree/main/notebooks
"},{"location":"season/","title":"Slot: season (season)","text":"The season when sampling occurred. Any of the four periods into which the year is divided by the equinoxes and solstices. This field accepts terms listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).
URI: MIXS:0000829
"},{"location":"season/#inheritance","title":"Inheritance","text":"name: season\nannotations:\n expected_value:\n tag: expected_value\n value: NCIT:C94729\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The season when sampling occurred. Any of the four periods into which\n the year is divided by the equinoxes and solstices. This field accepts terms listed\n under season (http://purl.obolibrary.org/obo/NCIT_C94729).\ntitle: season\nexamples:\n- value: autumn [NCIT:C94733]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- season\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000829\nalias: season\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nTreatment involving an exposure to a particular season (e.g. Winter, summer, rabi, rainy etc.), treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment
URI: MIXS:0001068
"},{"location":"season_environment/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: season_environment\nannotations:\n expected_value:\n tag: expected_value\n value: seasonal environment name;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to a particular season (e.g. Winter,\n summer, rabi, rainy etc.), treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment\ntitle: seasonal environment\nexamples:\n- value: rainy;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal environment\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001068\nalias: season_environment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps.
URI: MIXS:0000645
"},{"location":"season_precpt/#inheritance","title":"Inheritance","text":"name: season_precpt\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: millimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average of all seasonal precipitation values known, or an estimated\n equivalent value derived by such methods as regional indexes or Isohyetal maps.\ntitle: mean seasonal precipitation\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal precipitation\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000645\nalias: season_precpt\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMean seasonal temperature
URI: MIXS:0000643
"},{"location":"season_temp/#inheritance","title":"Inheritance","text":"name: season_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Mean seasonal temperature\ntitle: mean seasonal temperature\nexamples:\n- value: 18 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- mean seasonal temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000643\nalias: season_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe seasons the space is occupied
URI: MIXS:0000830
"},{"location":"season_use/#inheritance","title":"Inheritance","text":"name: season_use\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The seasons the space is occupied\ntitle: seasonal use\nexamples:\n- value: Winter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- seasonal use\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000830\nalias: season_use\ndomain_of:\n- Biosample\nrange: season_use_enum\nmultivalued: false\n\nThe process for substantially degrading the biological content of the sewage
URI: MIXS:0000351
"},{"location":"secondary_treatment/#inheritance","title":"Inheritance","text":"name: secondary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: secondary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process for substantially degrading the biological content of the\n sewage\ntitle: secondary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- secondary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000351\nalias: secondary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nInformation about the sediment type based on major constituents
URI: MIXS:0001078
"},{"location":"sediment_type/#inheritance","title":"Inheritance","text":"name: sediment_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Information about the sediment type based on major constituents\ntitle: sediment type\nexamples:\n- value: biogenous\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sediment type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001078\nalias: sediment_type\ndomain_of:\n- Biosample\nrange: sediment_type_enum\nmultivalued: false\n\nThe method that was used to separate a substance from a solution or mixture.
URI: nmdc:separation_method
"},{"location":"separation_method/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FiltrationProcess The process of segregation of phases; e no"},{"location":"separation_method/#properties","title":"Properties","text":"name: separation_method\ndescription: The method that was used to separate a substance from a solution or mixture.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: separation_method\ndomain_of:\n- FiltrationProcess\nrange: SeparationMethodEnum\n\nSequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).
URI: MIXS:0000050
"},{"location":"seq_meth/#inheritance","title":"Inheritance","text":"name: seq_meth\nannotations:\n expected_value:\n tag: expected_value\n value: Text or OBI\ndescription: Sequencing machine used. Where possible the term should be taken from\n the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).\ntitle: sequencing method\nexamples:\n- value: 454 Genome Sequencer FLX [OBI:0000702]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequencing method\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{termLabel} {[termID]}|{text}'\nslot_uri: MIXS:0000050\nalias: seq_meth\nrange: TextValue\nmultivalued: false\n\nIndicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA
URI: MIXS:0000051
"},{"location":"seq_quality_check/#inheritance","title":"Inheritance","text":"name: seq_quality_check\nannotations:\n expected_value:\n tag: expected_value\n value: none or manually edited\ndescription: Indicate if the sequence has been called by automatic systems (none)\n or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms).\n Applied only for sequences that are not submitted to SRA,ENA or DRA\ntitle: sequence quality check\nexamples:\n- value: none\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sequence quality check\nrank: 1000\nis_a: sequencing field\nstring_serialization: '[none|manually edited]'\nslot_uri: MIXS:0000051\nalias: seq_quality_check\nrange: TextValue\nmultivalued: false\n\nThe ID of the landmark used to establish the coordinate system for the current feature.
URI: nmdc:seqid
"},{"location":"seqid/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome yes"},{"location":"seqid/#properties","title":"Properties","text":"name: seqid\ndescription: The ID of the landmark used to establish the coordinate system for the\n current feature.\ntodos:\n- change range from string to object\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: seqid\ndomain_of:\n- GenomeFeature\nrange: string\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:sequencing_field
"},{"location":"sequencing_field/#inheritance","title":"Inheritance","text":"name: sequencing field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nabstract: true\nalias: sequencing_field\ndomain_of:\n- Biosample\nrange: string\n\nType of wastewater treatment plant as municipial or industrial
URI: MIXS:0000215
"},{"location":"sewage_type/#inheritance","title":"Inheritance","text":"name: sewage_type\nannotations:\n expected_value:\n tag: expected_value\n value: sewage type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Type of wastewater treatment plant as municipial or industrial\ntitle: sewage type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sewage type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000215\nalias: sewage_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSigns of the presence of mold or mildew on the shading device
URI: MIXS:0000834
"},{"location":"shad_dev_water_mold/#inheritance","title":"Inheritance","text":"name: shad_dev_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the shading device\ntitle: shading device signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000834\nalias: shad_dev_water_mold\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nThe physical condition of the shading device at the time of sampling
URI: MIXS:0000831
"},{"location":"shading_device_cond/#inheritance","title":"Inheritance","text":"name: shading_device_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the shading device at the time of sampling\ntitle: shading device condition\nexamples:\n- value: new\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000831\nalias: shading_device_cond\ndomain_of:\n- Biosample\nrange: shading_device_cond_enum\nmultivalued: false\n\nThe location of the shading device in relation to the built structure
URI: MIXS:0000832
"},{"location":"shading_device_loc/#inheritance","title":"Inheritance","text":"name: shading_device_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The location of the shading device in relation to the built structure\ntitle: shading device location\nexamples:\n- value: exterior\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device location\nrank: 1000\nis_a: core field\nstring_serialization: '[exterior|interior]'\nslot_uri: MIXS:0000832\nalias: shading_device_loc\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe material the shading device is composed of
URI: MIXS:0000245
"},{"location":"shading_device_mat/#inheritance","title":"Inheritance","text":"name: shading_device_mat\nannotations:\n expected_value:\n tag: expected_value\n value: material name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material the shading device is composed of\ntitle: shading device material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device material\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000245\nalias: shading_device_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe type of shading device
URI: MIXS:0000835
"},{"location":"shading_device_type/#inheritance","title":"Inheritance","text":"name: shading_device_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of shading device\ntitle: shading device type\nexamples:\n- value: slatted aluminum awning\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- shading device type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000835\nalias: shading_device_type\ndomain_of:\n- Biosample\nrange: shading_device_type_enum\nmultivalued: false\n\nCollection design of pooled samples and/or sieve size and amount of sample sieved
URI: MIXS:0000322
"},{"location":"sieving/#inheritance","title":"Inheritance","text":"name: sieving\nannotations:\n expected_value:\n tag: expected_value\n value: design name and/or size;amount\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Collection design of pooled samples and/or sieve size and amount of sample\n sieved\ntitle: composite design/sieving\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- composite design/sieving\nrank: 1000\nis_a: core field\nstring_serialization: '{{text}|{float} {unit}};{float} {unit}'\nslot_uri: MIXS:0000322\nalias: sieving\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nConcentration of silicate
URI: MIXS:0000184
"},{"location":"silicate/#inheritance","title":"Inheritance","text":"name: silicate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of silicate\ntitle: silicate\nexamples:\n- value: 0.05 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- silicate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000184\nalias: silicate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nFiltering pore size used in sample preparation
URI: MIXS:0000017
"},{"location":"size_frac/#inheritance","title":"Inheritance","text":"name: size_frac\nannotations:\n expected_value:\n tag: expected_value\n value: filter size value range\ndescription: Filtering pore size used in sample preparation\ntitle: size fraction selected\nexamples:\n- value: 0-0.22 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size fraction selected\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{float}-{float} {unit}'\nslot_uri: MIXS:0000017\nalias: size_frac\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nRefers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials larger than the size threshold are excluded from the sample
URI: MIXS:0000735
"},{"location":"size_frac_low/#inheritance","title":"Inheritance","text":"name: size_frac_low\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.\n Materials larger than the size threshold are excluded from the sample\ntitle: size-fraction lower threshold\nexamples:\n- value: 0.2 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction lower threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000735\nalias: size_frac_low\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nRefers to the mesh/pore size used to retain the sample. Materials smaller than the size threshold are excluded from the sample
URI: MIXS:0000736
"},{"location":"size_frac_up/#inheritance","title":"Inheritance","text":"name: size_frac_up\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: micrometer\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Refers to the mesh/pore size used to retain the sample. Materials smaller\n than the size threshold are excluded from the sample\ntitle: size-fraction upper threshold\nexamples:\n- value: 20 micrometer\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- size-fraction upper threshold\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000736\nalias: size_frac_up\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.
URI: MIXS:0000647
"},{"location":"slope_aspect/#inheritance","title":"Inheritance","text":"name: slope_aspect\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The direction a slope faces. While looking down a slope use a compass\n to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees.\n This measure provides an indication of sun and wind exposure that will influence\n soil temperature and evapotranspiration.\ntitle: slope aspect\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope aspect\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000647\nalias: slope_aspect\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCommonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer
URI: MIXS:0000646
"},{"location":"slope_gradient/#inheritance","title":"Inheritance","text":"name: slope_gradient\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Commonly called 'slope'. The angle between ground surface and a horizontal\n line (in percent). This is the direction that overland water would flow. This measure\n is usually taken with a hand level meter or clinometer\ntitle: slope gradient\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- slope gradient\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000646\nalias: slope_gradient\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe time activated sludge remains in reactor
URI: MIXS:0000669
"},{"location":"sludge_retent_time/#inheritance","title":"Inheritance","text":"name: sludge_retent_time\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: hours\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The time activated sludge remains in reactor\ntitle: sludge retention time\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sludge retention time\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000669\nalias: sludge_retent_time\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nA string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.
URI: nmdc:smiles
"},{"location":"smiles/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: smiles\ndescription: A string encoding of a molecular graph, no chiral or isotopic information.\n There are usually a large number of valid SMILES which represent a given structure.\n For example, CCO, OCC and C(O)C all specify the structure of ethanol.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: smiles\nrange: string\nmultivalued: true\n\nSodium concentration in the sample
URI: MIXS:0000428
"},{"location":"sodium/#inheritance","title":"Inheritance","text":"name: sodium\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Sodium concentration in the sample\ntitle: sodium\nexamples:\n- value: 10.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sodium\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000428\nalias: sodium\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nURI: nmdc:soil_annual_season_temp
"},{"location":"soil_annual_season_temp/#properties","title":"Properties","text":"name: soil_annual_season_temp\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soil_annual_season_temp\nrange: string\n\nSpecific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath
URI: MIXS:0001082
"},{"location":"soil_horizon/#inheritance","title":"Inheritance","text":"name: soil_horizon\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Specific layer in the land area which measures parallel to the soil surface\n and possesses physical characteristics which differ from the layers above and beneath\ntitle: soil horizon\nexamples:\n- value: A horizon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil horizon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001082\nalias: soil_horizon\ndomain_of:\n- Biosample\nrange: soil_horizon_enum\nmultivalued: false\n\nThe relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional.
URI: MIXS:0000335
"},{"location":"soil_text_measure/#inheritance","title":"Inheritance","text":"name: soil_text_measure\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative proportion of different grain sizes of mineral particles\n in a soil, as described using a standard system; express as % sand (50 um to 2 mm),\n silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam)\n optional.\ntitle: soil texture measurement\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture measurement\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000335\nalias: soil_text_measure\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining soil texture
URI: MIXS:0000336
"},{"location":"soil_texture_meth/#inheritance","title":"Inheritance","text":"name: soil_texture_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining soil texture\ntitle: soil texture method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil texture method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000336\nalias: soil_texture_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nDescription of the soil type or classification. This field accepts terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be separated by pipes.
URI: MIXS:0000332
"},{"location":"soil_type/#inheritance","title":"Inheritance","text":"name: soil_type\nannotations:\n expected_value:\n tag: expected_value\n value: ENVO_00001998\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of the soil type or classification. This field accepts terms\n under soil (http://purl.obolibrary.org/obo/ENVO_00001998). Multiple terms can be\n separated by pipes.\ntitle: soil type\nexamples:\n- value: plinthosol [ENVO:00002250]\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type\nrank: 1000\nis_a: core field\nstring_serialization: '{termLabel} {[termID]}'\nslot_uri: MIXS:0000332\nalias: soil_type\ndomain_of:\n- FieldResearchSite\n- Biosample\nrange: TextValue\nmultivalued: false\n\nReference or method used in determining soil series name or other lower-level classification
URI: MIXS:0000334
"},{"location":"soil_type_meth/#inheritance","title":"Inheritance","text":"name: soil_type_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining soil series name or other lower-level\n classification\ntitle: soil type method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soil type method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000334\nalias: soil_type_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe amount of solar energy that arrives at a specific area of a surface during a specific time interval
URI: MIXS:0000112
"},{"location":"solar_irradiance/#inheritance","title":"Inheritance","text":"name: solar_irradiance\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: kilowatts per square meter per day, ergs per square centimeter per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The amount of solar energy that arrives at a specific area of a surface\n during a specific time interval\ntitle: solar irradiance\nexamples:\n- value: 1.36 kilowatts per square meter per day\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- solar irradiance\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000112\nalias: solar_irradiance\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of substances such as ammonia, road-salt, sea-salt, cyanide, hydrogen sulfide, thiocyanates, thiosulfates, etc.
URI: MIXS:0000672
"},{"location":"soluble_inorg_mat/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: soluble_inorg_mat\nannotations:\n expected_value:\n tag: expected_value\n value: soluble inorganic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances such as ammonia, road-salt, sea-salt, cyanide,\n hydrogen sulfide, thiocyanates, thiosulfates, etc.\ntitle: soluble inorganic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble inorganic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000672\nalias: soluble_inorg_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:soluble_iron_micromol
"},{"location":"soluble_iron_micromol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"soluble_iron_micromol/#properties","title":"Properties","text":"name: soluble_iron_micromol\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: soluble_iron_micromol\ndomain_of:\n- Biosample\nrange: string\n\nConcentration of substances such as urea, fruit sugars, soluble proteins, drugs, pharmaceuticals, etc.
URI: MIXS:0000673
"},{"location":"soluble_org_mat/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: soluble_org_mat\nannotations:\n expected_value:\n tag: expected_value\n value: soluble organic material name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, mole per liter, gram per liter, parts per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances such as urea, fruit sugars, soluble proteins,\n drugs, pharmaceuticals, etc.\ntitle: soluble organic material\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble organic material\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000673\nalias: soluble_org_mat\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of soluble reactive phosphorus
URI: MIXS:0000738
"},{"location":"soluble_react_phosp/#inheritance","title":"Inheritance","text":"name: soluble_react_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of soluble reactive phosphorus\ntitle: soluble reactive phosphorus\nexamples:\n- value: 0.1 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- soluble reactive phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000738\nalias: soluble_react_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nWhen solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in solution A
URI: nmdc:source_concentration
"},{"location":"source_concentration/#inheritance","title":"Inheritance","text":"name: source_concentration\ndescription: When solutions A (containing substance X) and B are combined together,\n this slot captures the concentration of X in solution A\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: concentration\nalias: source_concentration\ndomain_of:\n- PortionOfSubstance\nrange: QuantityValue\n\nA unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).
URI: MIXS:0000026
"},{"location":"source_mat_id/#inheritance","title":"Inheritance","text":"name: source_mat_id\nannotations:\n expected_value:\n tag: expected_value\n value: 'for cultures of microorganisms: identifiers for two culture collections;\n for other material a unique arbitrary identifer'\ndescription: A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID,\n and as opposed to a particular digital record of a material sample) used for extracting\n nucleic acids, and subsequent sequencing. The identifier can refer either to the\n original material collected or to any derived sub-samples. The INSDC qualifiers\n /specimen_voucher, /bio_material, or /culture_collection may or may not share the\n same value as the source_mat_id field. For instance, the /specimen_voucher qualifier\n and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen\n voucher and sampled tissue with the same identifier. However, the /culture_collection\n qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id\n would refer to an identifier from some derived culture from which the nucleic acids\n were extracted (e.g. xatc123 or ark:/2154/R2).\ntitle: source material identifiers\nexamples:\n- value: MPI012345\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source material identifiers\nrank: 1000\nis_a: nucleic acid sequence source field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000026\nalias: source_mat_id\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nCustomary or normal state of the space
URI: MIXS:0000770
"},{"location":"space_typ_state/#inheritance","title":"Inheritance","text":"name: space_typ_state\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Customary or normal state of the space\ntitle: space typical state\nexamples:\n- value: typically occupied\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- space typical state\nrank: 1000\nis_a: core field\nstring_serialization: '[typically occupied|typically unoccupied]'\nslot_uri: MIXS:0000770\nalias: space_typ_state\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe building specifications. If design is chosen, indicate phase: conceptual, schematic, design development, construction documents
URI: MIXS:0000836
"},{"location":"specific/#inheritance","title":"Inheritance","text":"name: specific\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'The building specifications. If design is chosen, indicate phase: conceptual,\n schematic, design development, construction documents'\ntitle: specifications\nexamples:\n- value: construction\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specifications\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000836\nalias: specific\ndomain_of:\n- Biosample\nrange: specific_enum\nmultivalued: false\n\nSpecific ecosystems represent specific features of the environment like aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific ecosystem is in position 5/5 in a GOLD path.
URI: nmdc:specific_ecosystem
"},{"location":"specific_ecosystem/#inheritance","title":"Inheritance","text":"name: specific_ecosystem\ndescription: Specific ecosystems represent specific features of the environment like\n aphotic zone in an ocean or gastric mucosa within a host digestive system. Specific\n ecosystem is in position 5/5 in a GOLD path.\ncomments:\n- Specific ecosystems help to define samples based on very specific characteristics\n of an environment under the five-level classification system.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://gold.jgi.doe.gov/help\nrank: 1000\nis_a: gold_path_field\nalias: specific_ecosystem\ndomain_of:\n- Biosample\n- Study\nrange: string\n\nThe mass of water vapour in a unit mass of moist air, usually expressed as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.
URI: MIXS:0000214
"},{"location":"specific_humidity/#inheritance","title":"Inheritance","text":"name: specific_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram of air, kilogram of air\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The mass of water vapour in a unit mass of moist air, usually expressed\n as grams of vapour per kilogram of air, or, in air conditioning, as grains per pound.\ntitle: specific humidity\nexamples:\n- value: 15 per kilogram of air\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- specific humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000214\nalias: specific_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSource rock depositional environment (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000996
"},{"location":"sr_dep_env/#inheritance","title":"Inheritance","text":"name: sr_dep_env\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Source rock depositional environment (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock depositional environment\nexamples:\n- value: Marine\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock depositional environment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000996\nalias: sr_dep_env\ndomain_of:\n- Biosample\nrange: sr_dep_env_enum\nmultivalued: false\n\nGeological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000997
"},{"location":"sr_geol_age/#inheritance","title":"Inheritance","text":"name: sr_geol_age\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Geological age of source rock (Additional info: https://en.wikipedia.org/wiki/Period_(geology)).\n If \"other\" is specified, please propose entry in \"additional info\" field'\ntitle: source rock geological age\nexamples:\n- value: Silurian\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock geological age\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000997\nalias: sr_geol_age\ndomain_of:\n- Biosample\nrange: sr_geol_age_enum\nmultivalued: false\n\nOrigin of kerogen. Type I: Algal (aquatic), Type II: planktonic and soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial) (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000994
"},{"location":"sr_kerog_type/#inheritance","title":"Inheritance","text":"name: sr_kerog_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Origin of kerogen. Type I: Algal (aquatic), Type II: planktonic and\n soft plant material (aquatic or terrestrial), Type III: terrestrial woody/ fibrous\n plant material (terrestrial), Type IV: oxidized recycled woody debris (terrestrial)\n (additional information: https://en.wikipedia.org/wiki/Kerogen). If \"other\" is specified,\n please propose entry in \"additional info\" field'\ntitle: source rock kerogen type\nexamples:\n- value: Type IV\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock kerogen type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000994\nalias: sr_kerog_type\ndomain_of:\n- Biosample\nrange: sr_kerog_type_enum\nmultivalued: false\n\nLithology of source rock (https://en.wikipedia.org/wiki/Source_rock). If \"other\" is specified, please propose entry in \"additional info\" field
URI: MIXS:0000995
"},{"location":"sr_lithology/#inheritance","title":"Inheritance","text":"name: sr_lithology\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Lithology of source rock (https://en.wikipedia.org/wiki/Source_rock).\n If \"other\" is specified, please propose entry in \"additional info\" field\ntitle: source rock lithology\nexamples:\n- value: Coal\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- source rock lithology\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000995\nalias: sr_lithology\ndomain_of:\n- Biosample\nrange: sr_lithology_enum\nmultivalued: false\n\nTreatment involving an exposure to standing water during a plant's life span, types can be flood water or standing water, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0001069
"},{"location":"standing_water_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: standing_water_regm\nannotations:\n expected_value:\n tag: expected_value\n value: standing water type;treatment interval and duration\n occurrence:\n tag: occurrence\n value: m\ndescription: Treatment involving an exposure to standing water during a plant's life\n span, types can be flood water or standing water, treatment regimen including how\n many times the treatment was repeated, how long each treatment lasted, and the start\n and end time of the entire treatment; can include multiple regimens\ntitle: standing water regimen\nexamples:\n- value: standing water;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- standing water regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0001069\nalias: standing_water_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe start of the feature in positive 1-based integer coordinates
URI: nmdc:start
"},{"location":"start/#inheritance","title":"Inheritance","text":"Range: Integer
Minimum Value: 1
name: start\ndescription: The start of the feature in positive 1-based integer coordinates\nfrom_schema: https://w3id.org/nmdc/nmdc\nclose_mappings:\n- biolink:start_interbase_coordinate\nrank: 1000\nis_a: gff_coordinate\nalias: start\ndomain_of:\n- GenomeFeature\nrange: integer\nminimum_value: 1\n\nThe date on which any process or activity was started
URI: nmdc:start_date
"},{"location":"start_date/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no MetabolomicsAnalysis no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no NomAnalysis no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no PlannedProcess no StorageProcess A planned process with the objective to preserve and protect material entitie... no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no FiltrationProcess The process of segregation of phases; e no MetatranscriptomeAnnotation no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no Pooling physical combination of several instances of like material no CollectingBiosamplesFromSite no MetaproteomicsAnalysis no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no MetatranscriptomeAssembly no Extraction A material separation in which a desired component of an input material is se... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no ProtocolExecution A PlannedProces that has PlannedProcess parts no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no LibraryPreparation no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no"},{"location":"start_date/#properties","title":"Properties","text":"name: start_date\ndescription: The date on which any process or activity was started\ntodos:\n- add date string validation pattern\ncomments:\n- We are using string representations of dates until all components of our ecosystem\n can handle ISO 8610 dates\n- The date should be formatted as YYYY-MM-DD\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: start_date\ndomain_of:\n- PlannedProcess\nrange: string\n\nDate the incubation was started. Only relevant for incubation samples.
URI: nmdc:start_date_inc
"},{"location":"start_date_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_date_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: start_date_inc\ndescription: Date the incubation was started. Only relevant for incubation samples.\ntitle: incubation start date\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking arbitrary precision\n date only\ncomments:\n- Date should be formatted as YYYY(-MM(-DD)). Ie, 2021-04-15, 2021-04 and 2021 are\n all acceptable.\nexamples:\n- value: '2021-04-15'\n- value: 2021-04\n- value: '2021'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 4\nstring_serialization: '{date, arbitrary precision}'\nalias: start_date_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nTime the incubation was started. Only relevant for incubation samples.
URI: nmdc:start_time_inc
"},{"location":"start_time_inc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"start_time_inc/#properties","title":"Properties","text":"Range: String
Recommended: True
name: start_time_inc\ndescription: Time the incubation was started. Only relevant for incubation samples.\ntitle: incubation start time, GMT\nnotes:\n- MIxS collection_date accepts (truncated) ISO8601. DH taking seconds optional time\n only\ncomments:\n- 'Time should be entered as HH:MM(:SS) in GMT. See here for a converter: https://www.worldtimebuddy.com/pst-to-gmt-converter'\nexamples:\n- value: '13:33'\n- value: '13:33:55'\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- MIXS:0000011\nrank: 5\nstring_serialization: '{time, seconds optional}'\nalias: start_time_inc\ndomain_of:\n- Biosample\nslot_group: MIxS Inspired\nrange: string\nrecommended: true\n\nURI: nmdc:started_at_time
"},{"location":"started_at_time/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no NomAnalysis no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetaproteomicsAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no WorkflowExecution Represents an instance of an execution of a particular workflow yes MetatranscriptomeAssembly no"},{"location":"started_at_time/#properties","title":"Properties","text":"Range: String
Regex pattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$
name: started_at_time\nnotes:\n- 'The regex for ISO-8601 format was taken from here: https://www.myintervals.com/blog/2009/05/20/iso-8601-date-validation-that-doesnt-suck/\n It may not be complete, but it is good enough for now.'\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:startedAtTime\nrank: 1000\nalias: started_at_time\ndomain_of:\n- WorkflowExecution\nrange: string\npattern: ^([\\+-]?\\d{4}(?!\\d{2}\\b))((-?)((0[1-9]|1[0-2])(\\3([12]\\d|0[1-9]|3[01]))?|W([0-4]\\d|5[0-2])(-?[1-7])?|(00[1-9]|0[1-9]\\d|[12]\\d{2}|3([0-5]\\d|6[1-6])))([T\\s]((([01]\\d|2[0-3])((:?)[0-5]\\d)?|24\\:?00)([\\.,]\\d+(?!:))?)?(\\17[0-5]\\d([\\.,]\\d+)?)?([zZ]|([\\+-])([01]\\d|2[0-3]):?([0-5]\\d)?)?)?)?$\n\nThe material the stationary phase is comprised of used in chromatography.
URI: nmdc:stationary_phase
"},{"location":"stationary_phase/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no"},{"location":"stationary_phase/#properties","title":"Properties","text":"name: stationary_phase\ndescription: The material the stationary phase is comprised of used in chromatography.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stationary_phase\ndomain_of:\n- ChromatographyConfiguration\n- ChromatographicSeparationProcess\nrange: StationaryPhaseEnum\n\nThis property links a database object to the set of storage processes within it.
URI: nmdc:storage_process_set
"},{"location":"storage_process_set/#inheritance","title":"Inheritance","text":"Range: StorageProcess
Multivalued: True
name: storage_process_set\ndescription: This property links a database object to the set of storage processes\n within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: storage_process_set\ndomain_of:\n- Database\nrange: StorageProcess\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nExplain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other).
URI: MIXS:0000327
"},{"location":"store_cond/#inheritance","title":"Inheritance","text":"name: store_cond\nannotations:\n expected_value:\n tag: expected_value\n value: storage condition type;duration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Explain how and for how long the soil sample was stored before DNA extraction\n (fresh/frozen/other).\ntitle: storage conditions\nexamples:\n- value: -20 degree Celsius freezer;P2Y10D\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- storage conditions\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{duration}'\nslot_uri: MIXS:0000327\nalias: store_cond\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe strand on which a feature is located. Has a value of '+' (sense strand or forward strand) or '-' (anti-sense strand or reverse strand).
URI: nmdc:strand
"},{"location":"strand/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot GenomeFeature A feature localized to an interval along a genome no"},{"location":"strand/#properties","title":"Properties","text":"name: strand\ndescription: The strand on which a feature is located. Has a value of '+' (sense strand\n or forward strand) or '-' (anti-sense strand or reverse strand).\ntodos:\n- set the range to an enum?\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- biolink:strand\nrank: 1000\nalias: strand\ndomain_of:\n- GenomeFeature\nrange: string\n\nLists the strand orientiation for a stranded RNA library preparation.
URI: nmdc:stranded_orientation
"},{"location":"stranded_orientation/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot LibraryPreparation no"},{"location":"stranded_orientation/#properties","title":"Properties","text":"name: stranded_orientation\ndescription: Lists the strand orientiation for a stranded RNA library preparation.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: stranded_orientation\ndomain_of:\n- LibraryPreparation\nrange: StrandedOrientationEnum\n\nThe type of research initiative
URI: nmdc:study_category
"},{"location":"study_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_category/#properties","title":"Properties","text":"Range: StudyCategoryEnum
Required: True
name: study_category\ndescription: The type of research initiative\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_category\ndomain_of:\n- Study\nrange: StudyCategoryEnum\nrequired: true\n\nNote
This is an abstract slot and should not be populated directly.
URI: nmdc:study_identifiers
"},{"location":"study_identifiers/#inheritance","title":"Inheritance","text":"Range: ExternalIdentifier
Multivalued: True
Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$
name: study_identifiers\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nis_a: external_database_identifiers\nabstract: true\nalias: study_identifiers\nrange: external_identifier\nmultivalued: true\npattern: ^[a-zA-Z0-9][a-zA-Z0-9_\\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\\-\\/\\.,]*$\n\nLinks a study to one or more images.
URI: nmdc:study_image
"},{"location":"study_image/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"study_image/#properties","title":"Properties","text":"Range: ImageValue
Multivalued: True
name: study_image\ndescription: Links a study to one or more images.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: study_image\ndomain_of:\n- Study\nrange: ImageValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThis property links a database object to the set of studies within it.
URI: nmdc:study_set
"},{"location":"study_set/#inheritance","title":"Inheritance","text":"Range: Study
Multivalued: True
name: study_set\ndescription: This property links a database object to the set of studies within it.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: study_set\ndomain_of:\n- Database\nrange: Study\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nURI: nmdc:subject
"},{"location":"subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot OntologyRelation A relationship between two ontology classes as specified either directly in t... no FunctionalAnnotation An assignment of a function term (e no"},{"location":"subject/#properties","title":"Properties","text":"name: subject\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subject\ndomain_of:\n- FunctionalAnnotation\n- OntologyRelation\nrange: GeneProduct\n\nThe role of a substance in a process
URI: nmdc:substance_role
"},{"location":"substance_role/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no"},{"location":"substance_role/#properties","title":"Properties","text":"name: substance_role\ndescription: The role of a substance in a process\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substance_role\ndomain_of:\n- PortionOfSubstance\nrange: SubstanceRoleEnum\n\nThe substances that are combined to enable a ChemicalConversionProcess.
URI: nmdc:substances_used
"},{"location":"substances_used/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no StorageProcess A planned process with the objective to preserve and protect material entitie... yes Extraction A material separation in which a desired component of an input material is se... no"},{"location":"substances_used/#properties","title":"Properties","text":"Range: PortionOfSubstance
Multivalued: True
name: substances_used\ndescription: The substances that are combined to enable a ChemicalConversionProcess.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substances_used\ndomain_of:\n- Extraction\n- StorageProcess\n- DissolvingProcess\n- ChemicalConversionProcess\n- MobilePhaseSegment\nrange: PortionOfSubstance\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe volume of the combined substances that was included in a ChemicalConversionProcess.
URI: nmdc:substances_volume
"},{"location":"substances_volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no"},{"location":"substances_volume/#properties","title":"Properties","text":"name: substances_volume\ndescription: The volume of the combined substances that was included in a ChemicalConversionProcess.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: substances_volume\ndomain_of:\n- ChemicalConversionProcess\nrange: QuantityValue\n\nThe substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level
URI: MIXS:0000767
"},{"location":"substructure_type/#inheritance","title":"Inheritance","text":"Range: SubstructureTypeEnum
Multivalued: True
name: substructure_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: The substructure or under building is that largely hidden section of\n the building which is built off the foundations to the ground floor level\ntitle: substructure type\nexamples:\n- value: basement\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- substructure type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000767\nalias: substructure_type\ndomain_of:\n- Biosample\nrange: substructure_type_enum\nmultivalued: true\n\nURI: nmdc:subsurface_depth
"},{"location":"subsurface_depth/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"subsurface_depth/#properties","title":"Properties","text":"name: subsurface_depth\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: subsurface_depth\ndomain_of:\n- Biosample\nrange: QuantityValue\n\nConcentration of sulfate in the sample
URI: MIXS:0000423
"},{"location":"sulfate/#inheritance","title":"Inheritance","text":"name: sulfate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of sulfate in the sample\ntitle: sulfate\nexamples:\n- value: 5 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000423\nalias: sulfate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nOriginal sulfate concentration in the hydrocarbon resource
URI: MIXS:0000407
"},{"location":"sulfate_fw/#inheritance","title":"Inheritance","text":"name: sulfate_fw\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original sulfate concentration in the hydrocarbon resource\ntitle: sulfate in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfate in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000407\nalias: sulfate_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of sulfide in the sample
URI: MIXS:0000424
"},{"location":"sulfide/#inheritance","title":"Inheritance","text":"name: sulfide\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of sulfide in the sample\ntitle: sulfide\nexamples:\n- value: 2 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- sulfide\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000424\nalias: sulfide\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nContaminant identified on surface
URI: MIXS:0000759
"},{"location":"surf_air_cont/#inheritance","title":"Inheritance","text":"Range: SurfAirContEnum
Multivalued: True
name: surf_air_cont\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Contaminant identified on surface\ntitle: surface-air contaminant\nexamples:\n- value: radon\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface-air contaminant\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000759\nalias: surf_air_cont\ndomain_of:\n- Biosample\nrange: surf_air_cont_enum\nmultivalued: true\n\nSurfaces: water activity as a function of air and material moisture
URI: MIXS:0000123
"},{"location":"surf_humidity/#inheritance","title":"Inheritance","text":"name: surf_humidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percentage\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Surfaces: water activity as a function of air and material moisture'\ntitle: surface humidity\nexamples:\n- value: 10%\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface humidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000123\nalias: surf_humidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSurface materials at the point of sampling
URI: MIXS:0000758
"},{"location":"surf_material/#inheritance","title":"Inheritance","text":"name: surf_material\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Surface materials at the point of sampling\ntitle: surface material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000758\nalias: surf_material\ndomain_of:\n- Biosample\nrange: surf_material_enum\nmultivalued: false\n\nWater held on a surface
URI: MIXS:0000128
"},{"location":"surf_moisture/#inheritance","title":"Inheritance","text":"name: surf_moisture\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: parts per million, gram per cubic meter, gram per square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water held on a surface\ntitle: surface moisture\nexamples:\n- value: 0.01 gram per square meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000128\nalias: surf_moisture\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nph measurement of surface
URI: MIXS:0000760
"},{"location":"surf_moisture_ph/#inheritance","title":"Inheritance","text":"name: surf_moisture_ph\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: ph measurement of surface\ntitle: surface moisture pH\nexamples:\n- value: '7'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface moisture pH\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000760\nalias: surf_moisture_ph\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\nTemperature of the surface at the time of sampling
URI: MIXS:0000125
"},{"location":"surf_temp/#inheritance","title":"Inheritance","text":"name: surf_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Temperature of the surface at the time of sampling\ntitle: surface temperature\nexamples:\n- value: 15 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- surface temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000125\nalias: surf_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of suspended particulate matter
URI: MIXS:0000741
"},{"location":"suspend_part_matter/#inheritance","title":"Inheritance","text":"name: suspend_part_matter\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of suspended particulate matter\ntitle: suspended particulate matter\nexamples:\n- value: 0.5 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended particulate matter\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000741\nalias: suspend_part_matter\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of substances including a wide variety of material, such as silt, decaying plant and animal matter; can include multiple substances
URI: MIXS:0000150
"},{"location":"suspend_solids/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: suspend_solids\nannotations:\n expected_value:\n tag: expected_value\n value: suspended solid name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram, microgram, milligram per liter, mole per liter, gram per liter, part\n per million\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of substances including a wide variety of material, such\n as silt, decaying plant and animal matter; can include multiple substances\ntitle: suspended solids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- suspended solids\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000150\nalias: suspend_solids\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nTotal Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)
URI: MIXS:0000120
"},{"location":"tan/#inheritance","title":"Inheritance","text":"name: tan\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total Acid Number\u00ac\u2020(TAN) is a measurement of acidity that is determined\n by the amount of\u00ac\u2020potassium hydroxide\u00ac\u2020in milligrams that is needed to neutralize\n the acids in one gram of oil.\u00ac\u2020It is an important quality measurement of\u00ac\u2020crude\n oil. (source: https://en.wikipedia.org/wiki/Total_acid_number)'\ntitle: total acid number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total acid number\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000120\nalias: tan\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTargeted gene or locus name for marker gene studies
URI: MIXS:0000044
"},{"location":"target_gene/#inheritance","title":"Inheritance","text":"name: target_gene\nannotations:\n expected_value:\n tag: expected_value\n value: gene name\ndescription: Targeted gene or locus name for marker gene studies\ntitle: target gene\nexamples:\n- value: 16S rRNA, 18S rRNA, nif, amoA, rpo\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target gene\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000044\nalias: target_gene\ndomain_of:\n- NucleotideSequencing\nrange: TargetGeneEnum\nmultivalued: false\n\nName of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA
URI: MIXS:0000045
"},{"location":"target_subfragment/#inheritance","title":"Inheritance","text":"name: target_subfragment\nannotations:\n expected_value:\n tag: expected_value\n value: gene fragment name\ndescription: Name of subfragment of a gene or locus. Important to e.g. identify special\n regions on marker genes like V6 on 16S rRNA\ntitle: target subfragment\nexamples:\n- value: V6, V9, ITS\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- target subfragment\nrank: 1000\nis_a: sequencing field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000045\nalias: target_subfragment\ndomain_of:\n- NucleotideSequencing\nrange: TextValue\nmultivalued: false\n\nIf sending technical replicates of the same sample, indicate the replicate count.
URI: nmdc:technical_reps
"},{"location":"technical_reps/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"technical_reps/#properties","title":"Properties","text":"Range: String
Recommended: True
name: technical_reps\ndescription: If sending technical replicates of the same sample, indicate the replicate\n count.\ntitle: number technical replicate\ncomments:\n- This field is only required when completing metadata for samples being submitted\n to EMSL for analyses.\nexamples:\n- value: '2'\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 5\nstring_serialization: '{integer}'\nalias: technical_reps\ndomain_of:\n- Biosample\nslot_group: EMSL\nrange: string\nrecommended: true\n\nTemperature of the sample at the time of sampling.
URI: MIXS:0000113
"},{"location":"temp/#inheritance","title":"Inheritance","text":"name: temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\ndescription: Temperature of the sample at the time of sampling.\ntitle: temperature\nexamples:\n- value: 25 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature\nrank: 1000\nis_a: environment field\nslot_uri: MIXS:0000113\nalias: temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe recorded temperature value at sampling time outside
URI: MIXS:0000197
"},{"location":"temp_out/#inheritance","title":"Inheritance","text":"name: temp_out\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The recorded temperature value at sampling time outside\ntitle: temperature outside house\nexamples:\n- value: 5 degree Celsius\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- temperature outside house\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000197\nalias: temp_out\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe value of a temperature measurement or temperature used in a process.
URI: nmdc:temperature
"},{"location":"temperature/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no StorageProcess A planned process with the objective to preserve and protect material entitie... no"},{"location":"temperature/#properties","title":"Properties","text":"name: temperature\ndescription: The value of a temperature measurement or temperature used in a process.\nnotes:\n- Not to be confused with the MIXS:0000113\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: temperature\ndomain_of:\n- ChromatographyConfiguration\n- SubSamplingProcess\n- StorageProcess\n- ChromatographicSeparationProcess\n- DissolvingProcess\n- ChemicalConversionProcess\nrange: QuantityValue\n\npointer to an ontology class
URI: nmdc:term
"},{"location":"term/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... yes ControlledTermValue A controlled term or class from an ontology no"},{"location":"term/#properties","title":"Properties","text":"name: term\ndescription: pointer to an ontology class\nnotes:\n- 'removed ''slot_uri: rdf:type'''\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: term\ndomain_of:\n- ControlledTermValue\nrange: OntologyClass\ninlined: true\n\nThe process providing a final treatment stage to raise the effluent quality before it is discharged to the receiving environment
URI: MIXS:0000352
"},{"location":"tertiary_treatment/#inheritance","title":"Inheritance","text":"name: tertiary_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: tertiary treatment type\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The process providing a final treatment stage to raise the effluent quality\n before it is discharged to the receiving environment\ntitle: tertiary treatment\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tertiary treatment\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000352\nalias: tertiary_treatment\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nStage of tide
URI: MIXS:0000750
"},{"location":"tidal_stage/#inheritance","title":"Inheritance","text":"name: tidal_stage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Stage of tide\ntitle: tidal stage\nexamples:\n- value: high tide\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tidal stage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000750\nalias: tidal_stage\ndomain_of:\n- Biosample\nrange: tidal_stage_enum\nmultivalued: false\n\nNote method(s) used for tilling
URI: MIXS:0001081
"},{"location":"tillage/#inheritance","title":"Inheritance","text":"Range: TillageEnum
Multivalued: True
name: tillage\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: m\ndescription: Note method(s) used for tilling\ntitle: history/tillage\nexamples:\n- value: chisel\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- history/tillage\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0001081\nalias: tillage\ndomain_of:\n- Biosample\nrange: tillage_enum\nmultivalued: true\n\nDescription of plant tissue culture growth media used
URI: MIXS:0001070
"},{"location":"tiss_cult_growth_med/#inheritance","title":"Inheritance","text":"name: tiss_cult_growth_med\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI,url or free text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Description of plant tissue culture growth media used\ntitle: tissue culture growth media\nexamples:\n- value: https://link.springer.com/content/pdf/10.1007/BF02796489.pdf\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- tissue culture growth media\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}|{text}'\nslot_uri: MIXS:0001070\nalias: tiss_cult_growth_med\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nA name given to the entity that differs from the name/label programmatically assigned to it. For example, when extracting study information for GOLD, the GOLD system has assigned a name/label. However, for display purposes, we may also wish the capture the title of the proposal that was used to fund the study.
URI: nmdc:title
"},{"location":"title/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Study A study summarizes the overall goal of a research initiative and outlines the... no"},{"location":"title/#properties","title":"Properties","text":"name: title\ndescription: A name given to the entity that differs from the name/label programmatically\n assigned to it. For example, when extracting study information for GOLD, the GOLD\n system has assigned a name/label. However, for display purposes, we may also wish\n the capture the title of the proposal that was used to fund the study.\nfrom_schema: https://w3id.org/nmdc/nmdc\nexact_mappings:\n- dcterms:title\nrank: 1000\nalias: title\ndomain_of:\n- Study\nrange: string\n\nConcentration of toluene in the sample
URI: MIXS:0000154
"},{"location":"toluene/#inheritance","title":"Inheritance","text":"name: toluene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of toluene in the sample\ntitle: toluene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- toluene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000154\nalias: toluene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nNumber of contigs which were excluded from binning for length.
URI: nmdc:too_short_contig_num
"},{"location":"too_short_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"too_short_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: too_short_contig_num\ndescription: Number of contigs which were excluded from binning for length.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: too_short_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nTotal carbon content
URI: MIXS:0000525
"},{"location":"tot_carb/#inheritance","title":"Inheritance","text":"name: tot_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total carbon content\ntitle: total carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000525\nalias: tot_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nMeasurement of total depth of water column
URI: MIXS:0000634
"},{"location":"tot_depth_water_col/#inheritance","title":"Inheritance","text":"name: tot_depth_water_col\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of total depth of water column\ntitle: total depth of water column\nexamples:\n- value: 500 meter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total depth of water column\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000634\nalias: tot_depth_water_col\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen
URI: MIXS:0000744
"},{"location":"tot_diss_nitro/#inheritance","title":"Inheritance","text":"name: tot_diss_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total dissolved nitrogen concentration, reported as nitrogen, measured\n by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen'\ntitle: total dissolved nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total dissolved nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000744\nalias: tot_diss_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal inorganic nitrogen content
URI: MIXS:0000745
"},{"location":"tot_inorg_nitro/#inheritance","title":"Inheritance","text":"name: tot_inorg_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total inorganic nitrogen content\ntitle: total inorganic nitrogen\nexamples:\n- value: 40 microgram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total inorganic nitrogen\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000745\nalias: tot_inorg_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of total iron in the sample
URI: MIXS:0000105
"},{"location":"tot_iron/#inheritance","title":"Inheritance","text":"name: tot_iron\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, milligram per kilogram\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of total iron in the sample\ntitle: total iron\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total iron\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000105\nalias: tot_iron\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen
URI: MIXS:0000102
"},{"location":"tot_nitro/#inheritance","title":"Inheritance","text":"name: tot_nitro\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total nitrogen concentration of water samples, calculated by: total\n nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured\n without filtering, reported as nitrogen'\ntitle: total nitrogen concentration\nexamples:\n- value: 50 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen concentration\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000102\nalias: tot_nitro\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining the total nitrogen
URI: MIXS:0000338
"},{"location":"tot_nitro_cont_meth/#inheritance","title":"Inheritance","text":"name: tot_nitro_cont_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the total nitrogen\ntitle: total nitrogen content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000338\nalias: tot_nitro_cont_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nTotal nitrogen content of the sample
URI: MIXS:0000530
"},{"location":"tot_nitro_content/#inheritance","title":"Inheritance","text":"name: tot_nitro_content\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter, milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total nitrogen content of the sample\ntitle: total nitrogen content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total nitrogen content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000530\nalias: tot_nitro_content\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nReference or method used in determining total organic carbon
URI: MIXS:0000337
"},{"location":"tot_org_c_meth/#inheritance","title":"Inheritance","text":"name: tot_org_c_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining total organic carbon\ntitle: total organic carbon method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000337\nalias: tot_org_c_meth\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDefinition for soil: total organic carbon content of the soil, definition otherwise: total organic carbon content
URI: MIXS:0000533
"},{"location":"tot_org_carb/#inheritance","title":"Inheritance","text":"name: tot_org_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram Carbon per kilogram sample material\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Definition for soil: total organic carbon content of the soil, definition\n otherwise: total organic carbon content'\ntitle: total organic carbon\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total organic carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000533\nalias: tot_org_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal particulate carbon content
URI: MIXS:0000747
"},{"location":"tot_part_carb/#inheritance","title":"Inheritance","text":"name: tot_part_carb\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total particulate carbon content\ntitle: total particulate carbon\nexamples:\n- value: 35 micromole per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total particulate carbon\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000747\nalias: tot_part_carb\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus
URI: MIXS:0000117
"},{"location":"tot_phosp/#inheritance","title":"Inheritance","text":"name: tot_phosp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: micromole per liter, milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'Total phosphorus concentration in the sample, calculated by: total phosphorus\n = total dissolved phosphorus + particulate phosphorus'\ntitle: total phosphorus\nexamples:\n- value: 0.03 milligram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphorus\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000117\nalias: tot_phosp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal amount or concentration of phosphate
URI: MIXS:0000689
"},{"location":"tot_phosphate/#inheritance","title":"Inheritance","text":"name: tot_phosphate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per liter, micromole per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Total amount or concentration of phosphate\ntitle: total phosphate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total phosphate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000689\nalias: tot_phosphate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of total sulfur in the sample
URI: MIXS:0000419
"},{"location":"tot_sulfur/#inheritance","title":"Inheritance","text":"name: tot_sulfur\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of total sulfur in the sample\ntitle: total sulfur\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- total sulfur\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000419\nalias: tot_sulfur\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTotal number of basepairs.
URI: nmdc:total_bases
"},{"location":"total_bases/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagBin no"},{"location":"total_bases/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: total_bases\ndescription: Total number of basepairs.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: total_bases\ndomain_of:\n- MagBin\nrange: integer\nminimum_value: 0\n\nThe subway line name
URI: MIXS:0000837
"},{"location":"train_line/#inheritance","title":"Inheritance","text":"name: train_line\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The subway line name\ntitle: train line\nexamples:\n- value: red\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train line\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000837\nalias: train_line\ndomain_of:\n- Biosample\nrange: train_line_enum\nmultivalued: false\n\nThe train station collection location
URI: MIXS:0000838
"},{"location":"train_stat_loc/#inheritance","title":"Inheritance","text":"name: train_stat_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The train station collection location\ntitle: train station collection location\nexamples:\n- value: forest hills\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train station collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000838\nalias: train_stat_loc\ndomain_of:\n- Biosample\nrange: train_stat_loc_enum\nmultivalued: false\n\nThe train stop collection location
URI: MIXS:0000839
"},{"location":"train_stop_loc/#inheritance","title":"Inheritance","text":"name: train_stop_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The train stop collection location\ntitle: train stop collection location\nexamples:\n- value: end\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- train stop collection location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000839\nalias: train_stop_loc\ndomain_of:\n- Biosample\nrange: train_stop_loc_enum\nmultivalued: false\n\nMeasure of the amount of cloudiness or haziness in water caused by individual particles
URI: MIXS:0000191
"},{"location":"turbidity/#inheritance","title":"Inheritance","text":"name: turbidity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: formazin turbidity unit, formazin nephelometric units\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measure of the amount of cloudiness or haziness in water caused by individual\n particles\ntitle: turbidity\nexamples:\n- value: 0.3 nephelometric turbidity units\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- turbidity\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000191\nalias: turbidity\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTrue vertical depth subsea (TVDSS) of the hydrocarbon resource where the original pressure was measured (e.g. 1578 m).
URI: MIXS:0000397
"},{"location":"tvdss_of_hcr_press/#inheritance","title":"Inheritance","text":"name: tvdss_of_hcr_press\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original pressure was measured (e.g. 1578 m).\ntitle: depth (TVDSS) of hydrocarbon resource pressure\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource pressure\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000397\nalias: tvdss_of_hcr_press\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nTrue vertical depth subsea (TVDSS) of the hydrocarbon resource where the original temperature was measured (e.g. 1345 m).
URI: MIXS:0000394
"},{"location":"tvdss_of_hcr_temp/#inheritance","title":"Inheritance","text":"name: tvdss_of_hcr_temp\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: True vertical depth subsea (TVDSS) of the hydrocarbon resource where\n the original temperature was measured (e.g. 1345 m).\ntitle: depth (TVDSS) of hydrocarbon resource temperature\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- depth (TVDSS) of hydrocarbon resource temperature\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000394\nalias: tvdss_of_hcr_temp\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCustomary or normal density of occupants
URI: MIXS:0000771
"},{"location":"typ_occup_density/#inheritance","title":"Inheritance","text":"name: typ_occup_density\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Customary or normal density of occupants\ntitle: typical occupant density\nexamples:\n- value: '25'\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- typical occupant density\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000771\nalias: typ_occup_density\ndomain_of:\n- Biosample\nrange: double\nmultivalued: false\n\nthe class_uri of the class that has been instantiated
URI: rdf:type
"},{"location":"type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysis no NomAnalysis no GeolocationValue A normalized value for a location on the earth's surface no PlannedProcess no CalibrationInformation A calibration object that is associated with a process no NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated no CollectingBiosamplesFromSite no MixingProcess The combining of components, particles or layers into a more homogeneous stat... no EnvironmentalMaterialTerm no Extraction A material separation in which a desired component of an input material is se... no ControlledTermValue A controlled term or class from an ontology no ChemicalEntity An atom or molecule that can be represented with a chemical formula no MaterialEntity no PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no AttributeValue The value for any value of a attribute for a sample no OrthologyGroup A set of genes or gene products in which all members are orthologous no InformationObject Any data or knowledge that reduces uncertainty or enhances understanding abou... no ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent b... no MagBin no FailureCategorization no DataGeneration The methods and processes used to generate omics data from a biosample or org... no WorkflowExecution Represents an instance of an execution of a particular workflow no SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... no Study A study summarizes the overall goal of a research initiative and outlines the... no Site no MaterialProcessing A process that takes one or more samples as inputs and generates one or more ... no FiltrationProcess The process of segregation of phases; e no ImageValue An attribute value representing an image no MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are charac... no MetatranscriptomeAssembly no CreditAssociation This class supports binding associated researchers to studies no OntologyClass A representation of class defined in an external ontology no Configuration A set of parameters that define the actions of a process and is shared among ... no ProtocolExecution A PlannedProces that has PlannedProcess parts no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no ControlledIdentifiedTermValue A controlled term or class from an ontology, requiring the presence of term w... no ChemicalConversionProcess A process that results in the interconversion of chemical species by a reacti... no MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no DissolvingProcess A mixing step where a soluble component is mixed with a liquid component no TextValue A basic string value no StorageProcess A planned process with the objective to preserve and protect material entitie... no GeneProduct A molecule encoded by a gene that has an evolved function no MetatranscriptomeAnnotation no GenomeFeature A feature localized to an interval along a genome no MetaproteomicsAnalysis no Sample A sample is a material entity that can be characterized by an experiment no EukEval This class contains information pertaining to evaluating if a Metagenome-Asse... no Doi A centrally registered identifier symbol used to uniquely identify objects gi... no FunctionalAnnotationAggMember no MetaboliteIdentification This is used to link a metabolomics analysis workflow to a specific metabolit... no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no NamedThing a databased entity or concept/class no Manifest A qualified collection of DataObjects that can be analyzed together in the sa... no FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a func... no PersonValue An attribute value representing a person no ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography p... no DataObject An object that primarily consists of symbols that represent information no PeptideQuantification This is used to link a metaproteomics analysis workflow to a specific peptide... no FunctionalAnnotation An assignment of a function term (e no ProteinQuantification This is used to link a metaproteomics analysis workflow to a specific protein no FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected no ProcessedSample no Biosample Biological source material which can be characterized by an experiment no MetagenomeSequencing Initial sequencing activity that precedes any analysis no Pooling physical combination of several instances of like material no QuantityValue A simple quantity, e no Instrument A material entity that is designed to perform a function in a scientific inve... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no TimestampValue A value that is a timestamp no Pathway A pathway is a sequence of steps/reactions carried out by an organism or comm... no LibraryPreparation no Protocol no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass spectrometr... no OntologyRelation A relationship between two ontology classes as specified either directly in t... no"},{"location":"type/#properties","title":"Properties","text":"Range: Uriorcurie
Required: True
name: type\ndescription: the class_uri of the class that has been instantiated\nnotes:\n- replaces legacy nmdc:type slot\n- makes it easier to read example data files\n- required for polymorphic MongoDB collections\nexamples:\n- value: nmdc:Biosample\n- value: nmdc:Study\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://github.com/microbiomedata/nmdc-schema/issues/1048\n- https://github.com/microbiomedata/nmdc-schema/issues/1233\n- https://github.com/microbiomedata/nmdc-schema/issues/248\nstructured_aliases:\n workflow_execution_class:\n literal_form: workflow_execution_class\n predicate: NARROW_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\nrank: 1000\nslot_uri: rdf:type\ndesignates_type: true\nalias: type\ndomain_of:\n- EukEval\n- FunctionalAnnotationAggMember\n- PeptideQuantification\n- ProteinQuantification\n- MobilePhaseSegment\n- PortionOfSubstance\n- MagBin\n- MetaboliteIdentification\n- GenomeFeature\n- FunctionalAnnotation\n- AttributeValue\n- NamedThing\n- OntologyRelation\n- FailureCategorization\n- Protocol\n- CreditAssociation\n- Doi\nrange: uriorcurie\nrequired: true\n\nSchema class definitions include structured patterns that constrain the format of their id values. One element of the structured pattern is the typecode. The following table\u2014which was derived from the schema\u2014shows which schema class can have a given string in the typecode portion of its id values.
bsm Biosample calib CalibrationInformation chcpr ChemicalConversionProcess chrcon ChromatographyConfiguration clsite CollectingBiosamplesFromSite cspro ChromatographicSeparationProcess dgms, omprc MassSpectrometry dgns, omprc NucleotideSequencing dispro DissolvingProcess dobj DataObject extrp Extraction filtpr FiltrationProcess frsite FieldResearchSite inst Instrument libprp LibraryPreparation manif Manifest mixpro MixingProcess mscon MassSpectrometryConfiguration pex ProtocolExecution poolp Pooling procsm ProcessedSample storpr StorageProcess sty Study subspr SubSamplingProcess wfmag MagsAnalysis wfmb MetabolomicsAnalysis wfmgan MetagenomeAnnotation wfmgas MetagenomeAssembly wfmp MetaproteomicsAnalysis wfmsa MetagenomeSequencing wfmtan MetatranscriptomeAnnotation wfmtas MetatranscriptomeAssembly wfmtex MetatranscriptomeExpressionAnalysis wfnom NomAnalysis wfrbt ReadBasedTaxonomyAnalysis wfrqc ReadQcAnalysis"},{"location":"unbinned_contig_num/","title":"Slot: unbinned_contig_num","text":"Number of contigs which did not end up in a medium or high quality bin.
URI: nmdc:unbinned_contig_num
"},{"location":"unbinned_contig_num/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no"},{"location":"unbinned_contig_num/#properties","title":"Properties","text":"Range: Integer
Minimum Value: 0
name: unbinned_contig_num\ndescription: Number of contigs which did not end up in a medium or high quality bin.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: unbinned_contig_num\ndomain_of:\n- MagsAnalysis\nrange: integer\nminimum_value: 0\n\nURI: nmdc:url
"},{"location":"url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information no Protocol no ImageValue An attribute value representing an image no"},{"location":"url/#properties","title":"Properties","text":"name: url\nnotes:\n- See issue 207 - this clashes with the mixs field\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: url\ndomain_of:\n- ImageValue\n- Protocol\n- DataObject\nrange: string\n\ncalibration information is used by a process
URI: nmdc:uses_calibration
"},{"location":"uses_calibration/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetabolomicsAnalysis no NomAnalysis no"},{"location":"uses_calibration/#properties","title":"Properties","text":"name: uses_calibration\ndescription: calibration information is used by a process\ncomments:\n- Retenion index calibration data generated by a gas chromatography mass spectromery\n run is used when analyzing metabolomics data\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: uses_calibration\ndomain_of:\n- MetabolomicsAnalysis\n- NomAnalysis\nrange: CalibrationInformation\nstructured_pattern:\n syntax: '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'\n interpolated: true\n\nThis document is a retrospective on the changes made to the NMDC Schema between major versions 10 and 11.
Motivations for the Berkeley schema development included:
OmicsProcessing with DataGeneration\".See also: https://github.com/microbiomedata/nmdc-schema/releases/tag/v11.0.0
"},{"location":"v10-vs-v11-retrospective/#conventions","title":"Conventions:","text":"This monospaced code font is used to indicate the verbatim names of elements from the schema and variables, functions, etc. in code.UpperCamelCase are schema classes unless otherwise noted.lower_snake_case are schema slots unless otherwise noted.Vehicle.MotorVehicle.PassengerCar indicates a class hierarchy. PassengerCar is_a MotorVehicle and MotorVehicle is_a Vehicle.This major refactoring increases the number of classes in the schema from 70 to 75, but decreases the number of root classes from 19 to 17 due to better organization.
You won't find any classes designated as root classes in the schema, but they can be inferred by the absence of any is_a assertions on the class. Root classes do not inherit anything from any superclass. A routine part of schema maintenance is looking for opportunities to group and generalize similar root classes.
The Selected legacy parents column is provided to highlight two groups of updates that are discussed further below. Not every parent is shown for every legacy class.
Removed legacy class New/Replacement class from Berkeley schema Selected legacy parentsActivity AnalyticalSample BiosampleProcessing BooleanValue AttributeValue IntegerValue AttributeValue MagsAnalysisActivity MagsAnalysis WorkflowExecutionActivity MetaboliteQuantification MetaboliteIdentification MetabolomicsAnalysisActivity MetabolomicsAnalysis WorkflowExecutionActivity MetagenomeAnnotationActivity MetagenomeAnnotation WorkflowExecutionActivity MetagenomeSequencingActivity MetagenomeSequencing WorkflowExecutionActivity MetaproteomicsAnalysisActivity MetaproteomicsAnalysis WorkflowExecutionActivity MetatranscriptomeAnnotationActivity MetatranscriptomeAnnotation WorkflowExecutionActivity NomAnalysisActivity NomAnalysis WorkflowExecutionActivity OmicsProcessing DataGeneration Reaction ReactionParticipant ReadBasedTaxonomyAnalysisActivity ReadBasedTaxonomyAnalysis WorkflowExecutionActivity ReadQcAnalysisActivity ReadQcAnalysis WorkflowExecutionActivity Solution SolutionComponent UrlValue AttributeValue WorkflowExecutionActivity CalibrationInformation ChemicalConversionProcess ChromatographyConfiguration Configuration DissolvingProcess InformationObject Instrument MassSpectrometry MassSpectrometryConfiguration MaterialProcessing MobilePhaseSegment NucleotideSequencing PortionOfSubstance ProtocolExecution StorageProcess WorkflowExecution For example, the MetagenomeAnnotationActivity class used to be located in the hierarchy Activity.WorkFlowExecutionActivity, but now it and 11 similar classes are located in the hierarchy NamedThing.PlannedProcess.WorkflowExecution. The word Activity, inherited from the Provenance Ontology, has largely been removed from the schema, as PlannedProcess from the Ontology of Biomedical Investigations now plays a more important organizational role.
ProtocolExecution has been added as a PlannedProcess for aggregating other processes together when they follow the same Protocol.
Several other kinds of processual classes were also migrated into the NamedThing.PlannedProcess, with or without renaming or other refactoring. For example, the fairly vague root class OmicsProcessing is now NamedThing.PlannedProcess.DataGeneration, which now has the following subclasses:
MassSpectrometryNucleotideSequencingThe legacy BiosampleProcessing class (including Pooling, LibraryPreparation) and some classes that were previously direct subclasses of PlannedProcess (Extraction, SubSamplingProcess, MixingProcess, FiltrationProcess, ChromatographicSeparationProcess) have been re-rooted into a new MaterialProcessing class.
DissolvingProcess and ChemicalConversionProcess are new subclasses of MaterialProcessing.
StorageProcess has been added as a new PlannedProcess but the schema does not classify it as a MaterialProcessing because it does not intrinsically create new/modified samples.
Terms that implied quantification like MetaboliteQuantification have been renamed to reemphasize the more fundamental activity of identifying, thus MetaboliteIdentification.
A CalibrationInformation class, a Configuration class and two Configuration subclasses (illustrated below) have been added in support of chromatographic separations and mass spectrometry analyses. These are subclasses of the new InformationObject, which has also become the parent of DataObject, which used to be a direct subclass of NamedThing.
Solution-centric modelling for laboratory processes was also replaced with substance-centric modelling.
"},{"location":"v10-vs-v11-retrospective/#removed","title":"Removed:","text":"SolutionSolutionComponentPortionOfSubstanceMobilePhaseSegmentThe Berkeley schema retains the AttributeValue hierarchy but eliminates classes like IntegerValue and UrlValue, whose only advantages over values of integer or string types were never-used provenance slots.
Classes related to metabolic reactions that a cell could carry out, based on some functionality in its genome, have been removed, due to potential confusion with reactions that an experimenter might carry out in order to make a sample suitable for analysis.
"},{"location":"v10-vs-v11-retrospective/#removed_1","title":"Removed:","text":"ReactionReactionParticipantChemicalConversionProcessA very general Instrument class was added as a subclass of MaterialEntity, but without any subclasses. Knowledge about instruments is captured directly in NMDC's MongoDB database. The instances are normalized by populating their vendor slot with a value from the InstrumentVendorEnum and by populating the model slot with a value from the InstrumentModelEnum. Mappings between these NMDC vocabularies and vocabularies from collaborators like NCBI and GOLD are saved in various repos like nmdc-schema and nmdc-runtime.
AnalyticalSample was removed from the MaterialEntity hierarchy, as NMDC does not wish to imply that certain samples could be used for analyses or that others could not be used for analyses, or even that some samples are locked into an analytical path, such that they could not be subject to any more MaterialProcessing.
The number of slots in the schema remains 872 after the Berkeley merger, although there are 44 slots that have been retired from the legacy schema and 44 that were added in the switch from v10 to v11.
Many of the slot changes can be understood by looking at the Python data migration code in nmdc_schema/migrators.
A major explanation for the slot differences is the adoption of a polymorphic (i.e., multi-shaped) model for slots in the Database class, which corresponds to polymorphic collections in the v11-compliant MongoDB database. In the legacy model, the range for each of the Database slots was intended to be one class, with no provision for class hierarchy. In the new model, the range for each slot is still specified as a single class, but each Database slot can now collect instances of that specified class, plus the instances of any subclass of the specified class.
Database","text":"extraction_setlibrary_preparation_setmags_activity_setmetabolomics_analysis_activity_setmetagenome_annotation_activity_setmetagenome_assembly_setmetagenome_sequencing_activity_setmetaproteomics_analysis_activity_setmetatranscriptome_annotation_setmetatranscriptome_assembly_setmetatranscriptome_expression_analysis_setnom_analysis_activity_setomics_processing_setplanned_process_setpooling_setread_based_taxonomy_analysis_activity_setread_qc_analysis_activity_setDatabase","text":"calibration_setchemical_entity_setchromatographic_categoryconfiguration_setdata_generation_setinstrument_setmaterial_processing_setprotocol_execution_setstorage_process_setworkflow_execution_setSo now, instances of MetaproteomicsAnalysis, MetatranscriptomeAnnotation and NomAnalysis are all collected (or aggregated) in workflow_execution_set.
These polymorphic collection are enabled by a significant modeling change in v11 of the schema: a strict requirement that, within any representation of schema-compliant data, that all instances of all classes declare their own type. Furthermore, the values in the type slot must be the class_uri of the instantiated class. That, in turn, means that all classes must now declare a class_uri and that the type slots must be associated with each class. This is enforced with the following Python tests:
Note that classes should not re-associate themselves with any slot that they inherit from a superclass. For example, the class definition for Study inherits the id slot from NamedThing, so Study doesn't include id in its slots list. This no-reasserting rule is tested with test_inherited_slots_not_reiterated.py.
Also note that the legacy v10 schema did include a type slot, but it was used very inconsistently. v10 also had a similar designated_class slot which has been retired.
The following slots were removed as a consequence of removing the Reaction class and beginning the process of deprecating the Pathway class:
chemicaldirectionhas_parthas_participantsis_balancedis_diastereoselectiveis_fully_characterizedis_stereois_transportleft_participantsright_participantssmarts_stringstoichiometrycompound and has_solution_components were removed as a consequence of removing the Solution class.
The string-typed instrument_name and used were removed due to refactoring around the new Instrument class and the instrument_used slot, which is associated with numerous PlannedProcess subclasses.
The following changes have been made to slots in the Extraction class:
extractant was replaced with substances_usedextraction_method was replaced with protocol_linkextraction_target was replaced with a multivalued slot extraction_targetsThe string-typed relevant_protocols slot has been replaced with the protocol_link slot, which uses the Protocol class as its range.
The string-typed has_raw_value has been replaced with analyte_category, which has an enumerated range. The following are the permissible values for analyte_category:
metagenomemetatranscriptomemetaproteomemetabolomelipidomenomIn keeping with the focus on identification rather that quantification, has_metabolite_quantifications has been replaced with has_metabolite_identifications and metabolite_quantified has been replaced with metabolite_identified.
alternate_emails and keywords were removed due to lack of use.
The part_of slots have been replaced in many cases with more specific slots. For example, Biosample now has an associated_studies relationship with Study.
The NMDC Schema has always imported many slots from the MIxS standard, and has generally associated them with the Biosample class. In schema v11, several of those have been de-associated with Biosample as they are arguably attributes of laboratory methods, not about samples of biological materials that are extracted from some environment.
chimera_checknucl_acid_ampnucl_acid_extpcr_condpcr_primerspool_dna_extractssamp_vol_we_dna_extseq_methseq_quality_checktarget_genetarget_subfragmentSome, but not all, of those slots were re-associated with Extraction, LibraryPreparation, or NucleotideSequencing.
has_process_parts has been added to capture the relationship between a ProtocolExecution and the Process instances that were carried out with the intention of completing a specified protocol under specified circumstances.
The following slots have been added in support of the new CalibrationInformation and Configuration modelling for MassSpectrometry. The new schema's increased use of boolean and enumerated ranges (as opposed to open-ended string ranges) is nicely illustrated by these slots.
calibration_objectcalibration_standardcalibration_targetinternal_calibrationhas_chromatography_configurationhas_mass_spectrometry_configurationThe following slots have been added, specifically on MassSpectrometryConfiguration, so that a small number of MassSpectrometryConfiguration instances can be reused to describe the following:
mass_analyzersmass_spectrometry_acquisition_strategymass_spectrum_collection_modesionization_sourcepolarity_moderesolution_categoriesThese new slots are examplars of the increased emphasis on enumeration ranges (and the avoidance of the word 'type' in slot names other than type):
analyte_categorychemical_conversion_categorychromatographic_category applicable to ChromatographyConfiguration and ChromatographicSeparationProcess ?data_categoryeluent_introduction_categoryfeature_categoryprotocol_execution_categoryThe following new slots support the change from solution-based modeling to substance-based modelling:
substance_rolesubstances_usedsubstances_volumesource_concentrationfinal_concentrationsample_state_informationThe ChemicalEntity class has been refactored for nmdc-schema v11, and is likely to undergo additional changes in later 2024 and 2025. For now, a known_as slot has been added to allow for flexibility in PortionOfSubstance and retain precision in ChemicalEntity.
extraction_targets was added to Extraction. sampled_portion was added to SubSamplingProcess and jgi_portal_analysis_project_identifiers.
The following enumerations were removed:
CompoundEnumDeviceEnumprocessing_institution_enum was renamed to ProcessingInstitutionEnum.
And the following enumerations were added:
AnalyteCategoryEnumCalibrationStandardEnumCalibrationTargetEnumChemicalConversionCategoryEnumChromatographicCategoryEnumDataCategoryEnumEluentIntroductionCategoryEnumExecutionResourceEnumIonizationSourceEnumMassAnalyzerEnumMassSpectrometryAcquisitionStrategyEnumMassSpectrumCollectionModeEnumPolarityModeEnumProcessingInstitutionEnumProtocolCategoryEnumResolutionCategoryEnumSamplePortionEnumSampleStateEnumSubstanceRoleEnumExpansions for the following prefixes were added:
v10 of the schema provided 168 example data files. v11 has increased that to 224, providing better testing coverage of the schema via the run-linkml-example phase of make test.
v11 is also more thorough in annotating abstract classes, with 11, compared to 7 in v10. That includes a new abstract annotation for AttributeValue, MaterialProcessing (which essentially replaces BiosampleProcessing) and DataGeneration (which essentially replaces OmicsProcessing).
Running the whole schema though a tool like deepdiff can be overwhelming, but extracting a single class from two versions of the schema and then deep diffing them like this can be enlightening. Note that we are not curl-ing or wget-ing the schemas from GitHub, but rather using LinkML SchemaView() to fetch the root schema file and then merge in all of its imports.
The deepdiff results are then piped through yq with the -P option to convert to YAML. yq is distributed as a snap package in some Linux distributions, and snap applications can't generally write to standard output, so we add the otherwise redundant step of piping the output though cat in order to write to a file.
pre_schema.yaml:\n poetry run python -c 'from linkml_runtime.utils.schemaview import SchemaView; \\\n from linkml_runtime.dumpers import yaml_dumper; \\\n schema_url = \"https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v10.9.1/src/schema/nmdc.yaml\"; \\\n sv = SchemaView(schema_url, merge_imports=True); \\\n yaml_dumper.dump(sv.schema, \"pre_schema.yaml\")'\n\nberkeley_schema.yaml:\n poetry run python -c 'from linkml_runtime.utils.schemaview import SchemaView; \\\n from linkml_runtime.dumpers import yaml_dumper; \\\n schema_url = \"https://raw.githubusercontent.com/microbiomedata/nmdc-schema/refs/tags/v11.0.1/src/schema/nmdc.yaml\"; \\\n sv = SchemaView(schema_url, merge_imports=True); \\\n yaml_dumper.dump(sv.schema, \"berkeley_schema.yaml\")'\n\npre_study.yaml: pre_schema.yaml\n yq '.classes.Study' $< | cat > $@\n\nberkeley_study.yaml: berkeley_schema.yaml\n yq '.classes.Study' $< | cat > $@\n\npre_vs_berkeley_study.yaml: pre_study.yaml berkeley_study.yaml\n poetry run deep diff --ignore-order $^ | yq -P | cat > $@\ndictionary_item_added:\n - root['class_uri']\n - root['slot_usage']['protocol_link']\nvalues_changed:\n root['from_schema']:\n new_value: https://w3id.org/nmdc/basic_classes\n old_value: https://w3id.org/nmdc/nmdc\niterable_item_added:\n root['slots'][24]: protocol_link\niterable_item_removed:\n root['slots'][3]: id\n root['slots'][4]: alternative_identifiers\n root['slots'][9]: description\n root['slots'][26]: relevant_protocols\n root['slots'][30]: type\nThis reveals that the class_uri and protocol_link slots were added as described above. The from_schema values reveals the fact that v11 splits the elements of the schema into different YAML source files. The large number of files was intended to make it easier to debug build errors, but it has been difficult to split the contents into files that have a consistent domain or topic.
The diff also shows the removal of the id, alternative_identifiers, description, relevant_protocols and type slots, which might be counter-intuitive, until one considers that all of those slots are inherited from Study's parent, NamedThing and that schema v11 forbids re-asserting slots that are inherited from a superclass.
structured_patterns in slot_usages for approximating referential integrity, etc.","text":"LinkML slot definitions must assert their range, typically as a type (like string or float), an enumeration, or a class. If they don't, they inherit the schema's default_range, which is string in the nmdc-schema.
LinkML is able to validate that a slot, used in a data source (file or database collection), is populated with an entity of the right type (i.e. is in range) in almost all cases. Unfortunately, one of the cases that currently can not be validated is extremely important to NMDC: checking the data populated into a slot whose range is a non-inlined class. This case can also be described as the slot mentioning an instance of a class by reference. For the record, this requires that the mentioned class has an identifying slot of its own. An example of this is the associated_studies slot in the Biosample class, which has the Study class as its range. The definition of associated_studies does not assert inlined or inlined_as_list to be true, and the Study class inherits the id slot as an identifier from NamedThing. Therefore, the value of an associated_studies slot in a data file must be the id of a Study.
In the absense of any other data or constraints, the nmdc-schema will consider the following assertion valid for a Biosample, even if xyz isn't defined in the same data source:
associated_studies:\n - xyz\nIf xyz is defined in the data source and it does not pass validation as a Study, then the Biosample will also be considered invalid. Unfortunately, the definitions and mentions of nmdc-schema instances are frequently split across different MongoDB collections, so validating that a referred instance is really of the right type is non-trivial.
As a very lightweight guard against referring to instances of the wrong type, stuctured_patterns were added to slot_usages in berkeley-schema-fy24, and also independently in nmdc-schema v10 during the development of berkeley-schema-fy24/v11. In addition to being incomplete, this solution introduces some minor problems into the schema, and it relies on some other advanced LinkML features. Still, it has been useful in debugging some schema/data problems that slipped though the cracks in the past.
For example, the following can be found inside of Biosample's slot_usage block now:
associated_studies:\n required: true\n range: Study\n structured_pattern:\n syntax: \"{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$\"\n interpolated: true\nThat means that the value after associated_studies: in a Biosample must be the id of a Study instance, but also must be a string matching some pattern. The pattern is only revealed if all of the syntax elements in curly brackets are defined in the settings block of the schema, and if the schema has been fed though the gen-likml command line too with --materialize-patterns enabled. In the nmdc_schema/nmdc_materialized_patterns.yaml schema, one can see the intended pattern:
associated_studies:\n name: associated_studies\n range: Study\n required: true\n pattern: ^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$\n structured_pattern:\n syntax: '{id_nmdc_prefix}:sty-{id_shoulder}-{id_blade}$'\n interpolated: true\nTherefore, when using nmdc_schema/nmdc_materialized_patterns.yaml for validation, a Biosample with this assertion:
associated_studies:\n - xyz\nwould fail validation, because 'xyz' does not match '^(nmdc):sty-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,})$' (See https://regexr.com/87a0s). NMDC's use of structured_pattern slot_usages is a manual effort to align the id pattern specified in a class's definition with a constraint on how identifiers for instances of that class are mentioned in a slot.
Now that we have addressed structured_patterns including settings and gen-linkml, let's address slot_usages, which are attributes of LinkML classes that are intended to refine the behavior of slots, relative to their global definition within the schema. For example, here's the global definition of has_input:
has_input:\n aliases:\n - input\n range: NamedThing\n multivalued: true\n description: >-\n An input to a process.\nThe only constraint is that the value of has_input must be the id of a NamedThing, since has_input doesn't assert inlined or inlined_as_list, and NamedThing used id as it's identifying slot. As previously mentioned, structured_patterns can be used to improve the validation of this slot in some circumstances, but there are multiple classes that use has_input, and they don't all use the same range for has_input. For example, CollectingBiosamplesFromSite specifies that it's range for has_input is Site. Note that not all nmdc-schema contributors are in favor of those semantics.
has_input:\n range: Site\n description: >-\n The site from which samples are collected.\nThat slot_usage does not assert a structured_pattern, but many of them do. There are also classes that use has_input without any range constraint in their slot_usage, but might be clearer if they did. For example, WorkflowExecution should probably specify that it only uses DataObject in the range of its has_input. This would provide useful clarity to diagramming tools like refgraph.
Finally, we should point out that some slot_usage ranges in nmdc-schema use the LinkML any_of construct. For example, here's part of the slot_usage for MaterialProcessing:
has_input:\n any_of:\n - range: Biosample\n - range: ProcessedSample\n structured_pattern:\n syntax: \"{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$\"\n interpolated: true\nThat might be seen as asserting that MaterialProcessing's range is either Biosample or ProcessedSample, but has_input has the global range of NamedThing, so the effective range for has_input in MaterialProcessing is the union of NamedThing, Biosample and ProcessedSample.
Note that the slot_usage strucutred_pattern essentially asserts two different strucutured_pattern syntaxes, due to the use of the | character: \"{id_nmdc_prefix}:bsm-{id_shoulder}-{id_blade}$\" for Biosamples and \"{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$\" for ProcessedSamples.
slot_usage is complex to understand and use.structured_pattern requires the definition of settings and pattern materialization with gen-linkml in order to be useful.id patterns in class definitions, slot_usage structured_patterns, and slot_usage ranges.any_of ranges may not match LinkML's union-based understanding.any_of ranges can easily override global slot definitions, when they are meant to refine them (in the spirit of monotonicity).slot_usage structured_patterns, as used in the nmdc-schema, imply that the ranges of some slots are both a referred thing (asserted in the range), and a string (by way of the pattern). That can never be true, and it breaks the functionality of some derived artifacts, such as OWL and RDF.The LinkML and NMDC teams are currently working on more sophisticated solutions for interpreting any_of ranges, checking referential integrity and for making structured_pattern materialization the default in any situation that used the schema.
Please see LinkML Validation documentation for general information on validation with LinkML. It has several good examples of how to use linkml-validate in a python script or from the command line. https://linkml.io/linkml/data/validating-data.html
Using the examples in src/docs/examples, we can validate the data against the schema in python:
from linkml.validator import validate\n\ninstance = {\n \"id\": \"nmdc:bsm-99-dtTMNb\",\n \"associated_studies\": [\"nmdc:study-00-abc123\"],\n \"env_broad_scale\": {\n \"has_raw_value\": \"ENVO:00002030\",\n \"term\": {\n \"id\": \"ENVO:00002030\"\n }\n },\n \"env_local_scale\": {\n \"has_raw_value\": \"ENVO:00002169\",\n \"term\": {\n \"id\": \"ENVO:00002169\"\n }\n },\n \"env_medium\": {\n \"has_raw_value\": \"ENVO:00005792\",\n \"term\": {\n \"id\": \"ENVO:00005792\"\n }\n },\n \"type\": \"nmdc:Biosample\",\n \"analysis_type\": [\n \"amplicon sequencing assay\",\n \"metagenomics\"\n ]\n}\n\nreport = validate(instance, \"nmdc.yaml\", \"Biosample\")\n\nif not report.results:\n print('The instance is valid!')\nelse:\n for result in report.results:\n print(result.message)\nURI: nmdc:value
"},{"location":"value/#properties","title":"Properties","text":"name: value\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: value\nrange: QuantityValue\n\nURI: nmdc:vendor
"},{"location":"vendor/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Instrument A material entity that is designed to perform a function in a scientific inve... no"},{"location":"vendor/#properties","title":"Properties","text":"name: vendor\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: vendor\ndomain_of:\n- Instrument\nrange: InstrumentVendorEnum\n\nVentilation rate of the system in the sampled premises
URI: MIXS:0000114
"},{"location":"ventilation_rate/#inheritance","title":"Inheritance","text":"name: ventilation_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per minute, liters per second\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ventilation rate of the system in the sampled premises\ntitle: ventilation rate\nexamples:\n- value: 750 cubic meter per minute\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000114\nalias: ventilation_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nVentilation system used in the sampled premises
URI: MIXS:0000756
"},{"location":"ventilation_type/#inheritance","title":"Inheritance","text":"name: ventilation_type\nannotations:\n expected_value:\n tag: expected_value\n value: ventilation type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Ventilation system used in the sampled premises\ntitle: ventilation type\nexamples:\n- value: Operable windows\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- ventilation type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000756\nalias: ventilation_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:version
"},{"location":"version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAnnotation no MagsAnalysis A workflow execution activity that uses computational binning tools to group ... no ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... no ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... no MetabolomicsAnalysis no MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... no NomAnalysis no MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... no MetagenomeSequencing Initial sequencing activity that precedes any analysis no MetaproteomicsAnalysis no MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... no WorkflowExecution Represents an instance of an execution of a particular workflow no MetatranscriptomeAssembly no"},{"location":"version/#properties","title":"Properties","text":"name: version\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nalias: version\ndomain_of:\n- WorkflowExecution\nrange: string\n\nConcentration of Volatile Fatty Acids in the sample
URI: MIXS:0000152
"},{"location":"vfa/#inheritance","title":"Inheritance","text":"name: vfa\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of Volatile Fatty Acids in the sample\ntitle: volatile fatty acids\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile fatty acids\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000152\nalias: vfa\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nOriginal volatile fatty acid concentration in the hydrocarbon resource
URI: MIXS:0000408
"},{"location":"vfa_fw/#inheritance","title":"Inheritance","text":"name: vfa_fw\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Original volatile fatty acid concentration in the hydrocarbon resource\ntitle: vfa in formation water\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- vfa in formation water\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000408\nalias: vfa_fw\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe building visual media
URI: MIXS:0000840
"},{"location":"vis_media/#inheritance","title":"Inheritance","text":"name: vis_media\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building visual media\ntitle: visual media\nexamples:\n- value: 3D scans\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- visual media\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000840\nalias: vis_media\ndomain_of:\n- Biosample\nrange: vis_media_enum\nmultivalued: false\n\nA measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile stress (e.g. 3.5 cp; 100 \u00ac\u221eC)
URI: MIXS:0000126
"},{"location":"viscosity/#inheritance","title":"Inheritance","text":"name: viscosity\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;measurement value\n preferred_unit:\n tag: preferred_unit\n value: cP at degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: A measure of oil's resistance\u00ac\u2020to gradual deformation by\u00ac\u2020shear stress\u00ac\u2020or\u00ac\u2020tensile\n stress (e.g. 3.5 cp; 100 \u00ac\u221eC)\ntitle: viscosity\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- viscosity\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{float} {unit}'\nslot_uri: MIXS:0000126\nalias: viscosity\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThis inter-collection relationship diagram shows the database collections described by the schema, and the relationships between those collections.
Each circle represents a collection. Each arrow represents all of the fields that documents in one collection\u2014the one at that arrow's tail\u2014can use to refer to documents in another collection\u2014the one at that arrow's head. If you click on a circle, the names of the fields will appear on the arrows connected to that circle.
"},{"location":"volatile_org_comp/","title":"Slot: volatile organic compounds (volatile_org_comp)","text":"Concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound
URI: MIXS:0000115
"},{"location":"volatile_org_comp/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: volatile_org_comp\nannotations:\n expected_value:\n tag: expected_value\n value: volatile organic compound name;measurement value\n preferred_unit:\n tag: preferred_unit\n value: microgram per cubic meter, parts per million, nanogram per liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Concentration of carbon-based chemicals that easily evaporate at room\n temperature; can report multiple volatile organic compounds by entering numeric\n values preceded by name of compound\ntitle: volatile organic compounds\nexamples:\n- value: formaldehyde;500 nanogram per liter\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- volatile organic compounds\nrank: 1000\nis_a: core field\nstring_serialization: '{text};{float} {unit}'\nslot_uri: MIXS:0000115\nalias: volatile_org_comp\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nThe volume of a substance.
URI: nmdc:volume
"},{"location":"volume/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SubSamplingProcess Separating a sample aliquot from the starting material for downstream activit... yes FiltrationProcess The process of segregation of phases; e yes MobilePhaseSegment A fluid mixture of substances that flow though a chromatographic stationary p... no PortionOfSubstance A portion of any matter of defined composition that has discrete existence, w... no Extraction A material separation in which a desired component of an input material is se... yes"},{"location":"volume/#properties","title":"Properties","text":"name: volume\ndescription: The volume of a substance.\nfrom_schema: https://w3id.org/nmdc/nmdc\ncontributors:\n- ORCID:0009-0001-1555-1601\n- ORCID:0000-0002-8683-0050\nrank: 1000\nalias: volume\ndomain_of:\n- Extraction\n- SubSamplingProcess\n- FiltrationProcess\n- MobilePhaseSegment\n- PortionOfSubstance\nrange: QuantityValue\n\nThe total area of the sampled room's walls
URI: MIXS:0000198
"},{"location":"wall_area/#inheritance","title":"Inheritance","text":"name: wall_area\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The total area of the sampled room's walls\ntitle: wall area\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall area\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000198\nalias: wall_area\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe building class of the wall defined by the composition of the building elements and fire-resistance rating.
URI: MIXS:0000841
"},{"location":"wall_const_type/#inheritance","title":"Inheritance","text":"name: wall_const_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The building class of the wall defined by the composition of the building\n elements and fire-resistance rating.\ntitle: wall construction type\nexamples:\n- value: fire resistive\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall construction type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000841\nalias: wall_const_type\ndomain_of:\n- Biosample\nrange: wall_const_type_enum\nmultivalued: false\n\nThe material utilized to finish the outer most layer of the wall
URI: MIXS:0000842
"},{"location":"wall_finish_mat/#inheritance","title":"Inheritance","text":"name: wall_finish_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The material utilized to finish the outer most layer of the wall\ntitle: wall finish material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall finish material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000842\nalias: wall_finish_mat\ndomain_of:\n- Biosample\nrange: wall_finish_mat_enum\nmultivalued: false\n\nThe average height of the walls in the sampled room
URI: MIXS:0000221
"},{"location":"wall_height/#inheritance","title":"Inheritance","text":"name: wall_height\nannotations:\n expected_value:\n tag: expected_value\n value: value\n preferred_unit:\n tag: preferred_unit\n value: centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The average height of the walls in the sampled room\ntitle: wall height\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall height\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000221\nalias: wall_height\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe relative location of the wall within the room
URI: MIXS:0000843
"},{"location":"wall_loc/#inheritance","title":"Inheritance","text":"name: wall_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the wall within the room\ntitle: wall location\nexamples:\n- value: north\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000843\nalias: wall_loc\ndomain_of:\n- Biosample\nrange: wall_loc_enum\nmultivalued: false\n\nThe surface treatment of interior wall
URI: MIXS:0000845
"},{"location":"wall_surf_treatment/#inheritance","title":"Inheritance","text":"name: wall_surf_treatment\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The surface treatment of interior wall\ntitle: wall surface treatment\nexamples:\n- value: paneling\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall surface treatment\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000845\nalias: wall_surf_treatment\ndomain_of:\n- Biosample\nrange: wall_surf_treatment_enum\nmultivalued: false\n\nThe feel, appearance, or consistency of a wall surface
URI: MIXS:0000846
"},{"location":"wall_texture/#inheritance","title":"Inheritance","text":"name: wall_texture\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The feel, appearance, or consistency of a wall surface\ntitle: wall texture\nexamples:\n- value: popcorn\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall texture\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000846\nalias: wall_texture\ndomain_of:\n- Biosample\nrange: wall_texture_enum\nmultivalued: false\n\nThe ability of the wall to provide inertia against temperature fluctuations. Generally this means concrete or concrete block that is either exposed or covered only with paint
URI: MIXS:0000222
"},{"location":"wall_thermal_mass/#inheritance","title":"Inheritance","text":"name: wall_thermal_mass\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: joule per degree Celsius\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The ability of the wall to provide inertia against temperature fluctuations.\n Generally this means concrete or concrete block that is either exposed or covered\n only with paint\ntitle: wall thermal mass\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall thermal mass\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000222\nalias: wall_thermal_mass\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nSigns of the presence of mold or mildew on a wall
URI: MIXS:0000844
"},{"location":"wall_water_mold/#inheritance","title":"Inheritance","text":"name: wall_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on a wall\ntitle: wall signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wall signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000844\nalias: wall_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nURI: nmdc:was_generated_by
"},{"location":"was_generated_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DataObject An object that primarily consists of symbols that represent information yes FunctionalAnnotation An assignment of a function term (e yes FunctionalAnnotationAggMember yes"},{"location":"was_generated_by/#properties","title":"Properties","text":"name: was_generated_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nmappings:\n- prov:wasGeneratedBy\nrank: 1000\nalias: was_generated_by\ndomain_of:\n- FunctionalAnnotationAggMember\n- FunctionalAnnotation\n- DataObject\nrange: WorkflowExecution\nany_of:\n- range: WorkflowExecution\n- range: DataGeneration\n\nURI: nmdc:was_informed_by
"},{"location":"was_informed_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MetatranscriptomeAnnotation yes MagsAnalysis A workflow execution activity that uses computational binning tools to group ... yes ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina r... yes ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using seq... yes MetabolomicsAnalysis yes MetagenomeAssembly A workflow execution activity that converts sequencing reads into an assemble... yes NomAnalysis yes MetagenomeAnnotation A workflow execution activity that provides functional and structural annotat... yes MetagenomeSequencing Initial sequencing activity that precedes any analysis yes MetaproteomicsAnalysis yes MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene f... yes WorkflowExecution Represents an instance of an execution of a particular workflow yes MetatranscriptomeAssembly yes"},{"location":"was_informed_by/#properties","title":"Properties","text":"name: was_informed_by\nfrom_schema: https://w3id.org/nmdc/nmdc\nstructured_aliases:\n was_informed_by:\n literal_form: was_informed_by\n predicate: EXACT_SYNONYM\n contexts:\n - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml\nmappings:\n- prov:wasInformedBy\nrank: 1000\nalias: was_informed_by\ndomain_of:\n- WorkflowExecution\nrange: DataGeneration\n\nThe origin of wastewater such as human waste, rainfall, storm drains, etc.
URI: MIXS:0000353
"},{"location":"wastewater_type/#inheritance","title":"Inheritance","text":"name: wastewater_type\nannotations:\n expected_value:\n tag: expected_value\n value: wastewater type name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The origin of wastewater such as human waste, rainfall, storm drains,\n etc.\ntitle: wastewater type\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wastewater type\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000353\nalias: wastewater_type\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nReference or method used in determining the water content of soil
URI: MIXS:0000323
"},{"location":"water_cont_soil_meth/#inheritance","title":"Inheritance","text":"name: water_cont_soil_meth\nannotations:\n expected_value:\n tag: expected_value\n value: PMID,DOI or url\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Reference or method used in determining the water content of soil\ntitle: water content method\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content method\nrank: 1000\nis_a: core field\nstring_serialization: '{PMID}|{DOI}|{URL}'\nslot_uri: MIXS:0000323\nalias: water_cont_soil_meth\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nWater content measurement
URI: MIXS:0000185
"},{"location":"water_content/#inheritance","title":"Inheritance","text":"name: water_content\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: gram per gram or cubic centimeter per cubic centimeter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water content measurement\ntitle: water content\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water content\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000185\nalias: water_content\ndomain_of:\n- Biosample\nrange: string\nmultivalued: false\n\nMeasurement of magnitude and direction of flow within a fluid
URI: MIXS:0000203
"},{"location":"water_current/#inheritance","title":"Inheritance","text":"name: water_current\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per second, knots\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Measurement of magnitude and direction of flow within a fluid\ntitle: water current\nexamples:\n- value: 10 cubic meter per second\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water current\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000203\nalias: water_current\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nCurrent amount of water (%) in a produced fluid stream; or the average of the combined streams
URI: MIXS:0000454
"},{"location":"water_cut/#inheritance","title":"Inheritance","text":"name: water_cut\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: percent\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Current amount of water (%) in a produced fluid stream; or the average\n of the combined streams\ntitle: water cut\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water cut\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000454\nalias: water_cut\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe size of the water feature
URI: MIXS:0000223
"},{"location":"water_feat_size/#inheritance","title":"Inheritance","text":"name: water_feat_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: square meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The size of the water feature\ntitle: water feature size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature size\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000223\nalias: water_feat_size\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe type of water feature present within the building being sampled
URI: MIXS:0000847
"},{"location":"water_feat_type/#inheritance","title":"Inheritance","text":"name: water_feat_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of water feature present within the building being sampled\ntitle: water feature type\nexamples:\n- value: stream\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water feature type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000847\nalias: water_feat_type\ndomain_of:\n- Biosample\nrange: water_feat_type_enum\nmultivalued: false\n\nWater production rates per well (e.g. 987 m3 / day)
URI: MIXS:0000453
"},{"location":"water_prod_rate/#inheritance","title":"Inheritance","text":"name: water_prod_rate\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: cubic meter per day\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Water production rates per well (e.g. 987 m3 / day)\ntitle: water production rate\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water production rate\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000453\nalias: water_prod_rate\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nInformation about treatment involving an exposure to water with varying degree of temperature, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000590
"},{"location":"water_temp_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: water_temp_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: degree Celsius\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to water with varying\n degree of temperature, treatment regimen including how many times the treatment\n was repeated, how long each treatment lasted, and the start and end time of the\n entire treatment; can include multiple regimens\ntitle: water temperature regimen\nexamples:\n- value: 15 degree Celsius;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- water temperature regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000590\nalias: water_temp_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nInformation about treatment involving an exposure to watering frequencies, treatment regimen including how many times the treatment was repeated, how long each treatment lasted, and the start and end time of the entire treatment; can include multiple regimens
URI: MIXS:0000591
"},{"location":"watering_regm/#inheritance","title":"Inheritance","text":"Range: TextValue
Multivalued: True
name: watering_regm\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value;treatment interval and duration\n preferred_unit:\n tag: preferred_unit\n value: milliliter, liter\n occurrence:\n tag: occurrence\n value: m\ndescription: Information about treatment involving an exposure to watering frequencies,\n treatment regimen including how many times the treatment was repeated, how long\n each treatment lasted, and the start and end time of the entire treatment; can include\n multiple regimens\ntitle: watering regimen\nexamples:\n- value: 1 liter;R2/2018-05-11T14:30/2018-05-11T19:30/P1H30M\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- watering regimen\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'\nslot_uri: MIXS:0000591\nalias: watering_regm\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nA list of websites that are associated with the entity.
URI: nmdc:websites
"},{"location":"websites/#inheritance","title":"Inheritance","text":"Range: String
Multivalued: True
Regex pattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$
name: websites\ndescription: A list of websites that are associated with the entity.\ncomments:\n- DOIs should not be included as websites. Instead, use the associated_dois slot.\n- A consortium's homepage website should be included in the homepage_website slot,\n not in websites.\n- consortium is a convenience term for a Study whose study_category value is consortium\n- the website slot and its subproperties are virtually identical to the url slot,\n except that they are multivalued and url is single-valued.\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- nmdc:url\nrank: 1000\nalias: websites\ndomain_of:\n- PersonValue\n- Study\nrange: string\nmultivalued: true\npattern: ^[Hh][Tt][Tt][Pp][Ss]?:\\/\\/(?!.*[Dd][Oo][Ii]\\.[Oo][Rr][Gg]).*$\n\nThe day of the week when sampling occurred
URI: MIXS:0000848
"},{"location":"weekday/#inheritance","title":"Inheritance","text":"name: weekday\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The day of the week when sampling occurred\ntitle: weekday\nexamples:\n- value: Sunday\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- weekday\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000848\nalias: weekday\ndomain_of:\n- Biosample\nrange: weekday_enum\nmultivalued: false\n\nA unique identifier of a well or wellbore. This is part of the Global Framework for Well Identification initiative which is compiled by the Professional Petroleum Data Management Association (PPDM) in an effort to improve well identification systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)
URI: MIXS:0000297
"},{"location":"win/#inheritance","title":"Inheritance","text":"name: win\nannotations:\n expected_value:\n tag: expected_value\n value: text\n occurrence:\n tag: occurrence\n value: '1'\ndescription: 'A unique identifier of a well or wellbore. This is part of the Global\n Framework for Well Identification initiative which is compiled by the Professional\n Petroleum Data Management Association (PPDM) in an effort to improve well identification\n systems. (Supporting information: https://ppdm.org/ and http://dl.ppdm.org/dl/690)'\ntitle: well identification number\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- well identification number\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000297\nalias: win\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nWind direction is the direction from which a wind originates
URI: MIXS:0000757
"},{"location":"wind_direction/#inheritance","title":"Inheritance","text":"name: wind_direction\nannotations:\n expected_value:\n tag: expected_value\n value: wind direction name\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Wind direction is the direction from which a wind originates\ntitle: wind direction\nexamples:\n- value: Northwest\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind direction\nrank: 1000\nis_a: core field\nstring_serialization: '{text}'\nslot_uri: MIXS:0000757\nalias: wind_direction\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nSpeed of wind measured at the time of sampling
URI: MIXS:0000118
"},{"location":"wind_speed/#inheritance","title":"Inheritance","text":"name: wind_speed\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: meter per second, kilometer per hour\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Speed of wind measured at the time of sampling\ntitle: wind speed\nexamples:\n- value: 21 kilometer per hour\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- wind speed\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000118\nalias: wind_speed\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nThe physical condition of the window at the time of sampling
URI: MIXS:0000849
"},{"location":"window_cond/#inheritance","title":"Inheritance","text":"name: window_cond\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The physical condition of the window at the time of sampling\ntitle: window condition\nexamples:\n- value: rupture\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window condition\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000849\nalias: window_cond\ndomain_of:\n- Biosample\nrange: window_cond_enum\nmultivalued: false\n\nThe type of window covering
URI: MIXS:0000850
"},{"location":"window_cover/#inheritance","title":"Inheritance","text":"name: window_cover\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of window covering\ntitle: window covering\nexamples:\n- value: curtains\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window covering\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000850\nalias: window_cover\ndomain_of:\n- Biosample\nrange: window_cover_enum\nmultivalued: false\n\nThe horizontal position of the window on the wall
URI: MIXS:0000851
"},{"location":"window_horiz_pos/#inheritance","title":"Inheritance","text":"name: window_horiz_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The horizontal position of the window on the wall\ntitle: window horizontal position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window horizontal position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000851\nalias: window_horiz_pos\ndomain_of:\n- Biosample\nrange: window_horiz_pos_enum\nmultivalued: false\n\nThe relative location of the window within the room
URI: MIXS:0000852
"},{"location":"window_loc/#inheritance","title":"Inheritance","text":"name: window_loc\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The relative location of the window within the room\ntitle: window location\nexamples:\n- value: west\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window location\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000852\nalias: window_loc\ndomain_of:\n- Biosample\nrange: window_loc_enum\nmultivalued: false\n\nThe type of material used to finish a window
URI: MIXS:0000853
"},{"location":"window_mat/#inheritance","title":"Inheritance","text":"name: window_mat\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of material used to finish a window\ntitle: window material\nexamples:\n- value: wood\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window material\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000853\nalias: window_mat\ndomain_of:\n- Biosample\nrange: window_mat_enum\nmultivalued: false\n\nThe number of times windows are opened per week
URI: MIXS:0000246
"},{"location":"window_open_freq/#inheritance","title":"Inheritance","text":"name: window_open_freq\nannotations:\n expected_value:\n tag: expected_value\n value: value\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The number of times windows are opened per week\ntitle: window open frequency\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window open frequency\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000246\nalias: window_open_freq\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe window's length and width
URI: MIXS:0000224
"},{"location":"window_size/#inheritance","title":"Inheritance","text":"name: window_size\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: inch, meter\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The window's length and width\ntitle: window area/size\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window area/size\nrank: 1000\nis_a: core field\nstring_serialization: '{float} {unit} x {float} {unit}'\nslot_uri: MIXS:0000224\nalias: window_size\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nDefines whether the windows were open or closed during environmental testing
URI: MIXS:0000855
"},{"location":"window_status/#inheritance","title":"Inheritance","text":"name: window_status\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Defines whether the windows were open or closed during environmental\n testing\ntitle: window status\nexamples:\n- value: open\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window status\nrank: 1000\nis_a: core field\nstring_serialization: '[closed|open]'\nslot_uri: MIXS:0000855\nalias: window_status\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThe type of windows
URI: MIXS:0000856
"},{"location":"window_type/#inheritance","title":"Inheritance","text":"name: window_type\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The type of windows\ntitle: window type\nexamples:\n- value: fixed window\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window type\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000856\nalias: window_type\ndomain_of:\n- Biosample\nrange: window_type_enum\nmultivalued: false\n\nThe vertical position of the window on the wall
URI: MIXS:0000857
"},{"location":"window_vert_pos/#inheritance","title":"Inheritance","text":"name: window_vert_pos\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: The vertical position of the window on the wall\ntitle: window vertical position\nexamples:\n- value: middle\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window vertical position\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000857\nalias: window_vert_pos\ndomain_of:\n- Biosample\nrange: window_vert_pos_enum\nmultivalued: false\n\nSigns of the presence of mold or mildew on the window.
URI: MIXS:0000854
"},{"location":"window_water_mold/#inheritance","title":"Inheritance","text":"name: window_water_mold\nannotations:\n expected_value:\n tag: expected_value\n value: enumeration\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Signs of the presence of mold or mildew on the window.\ntitle: window signs of water/mold\nexamples:\n- value: no presence of mold visible\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- window signs of water/mold\nrank: 1000\nis_a: core field\nstring_serialization: '[presence of mold visible|no presence of mold visible]'\nslot_uri: MIXS:0000854\nalias: window_water_mold\ndomain_of:\n- Biosample\nrange: TextValue\nmultivalued: false\n\nThis property links a database object to the set of workflow executions.
URI: nmdc:workflow_execution_set
"},{"location":"workflow_execution_set/#inheritance","title":"Inheritance","text":"Range: WorkflowExecution
Multivalued: True
name: workflow_execution_set\ndescription: This property links a database object to the set of workflow executions.\nfrom_schema: https://w3id.org/nmdc/nmdc\nrank: 1000\nmixins:\n- object_set\nalias: workflow_execution_set\ndomain_of:\n- Database\nrange: WorkflowExecution\nmultivalued: true\ninlined: true\ninlined_as_list: true\n\nConcentration of xylene in the sample
URI: MIXS:0000156
"},{"location":"xylene/#inheritance","title":"Inheritance","text":"name: xylene\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: milligram per liter, parts per million\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of xylene in the sample\ntitle: xylene\nexamples:\n- value: ''\nfrom_schema: https://w3id.org/nmdc/nmdc\naliases:\n- xylene\nrank: 1000\nis_a: core field\nslot_uri: MIXS:0000156\nalias: xylene\ndomain_of:\n- Biosample\nrange: QuantityValue\nmultivalued: false\n\nConcentration of zinc in the sample
URI: nmdc:zinc
"},{"location":"zinc/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Biosample Biological source material which can be characterized by an experiment no"},{"location":"zinc/#properties","title":"Properties","text":"name: zinc\nannotations:\n expected_value:\n tag: expected_value\n value: measurement value\n preferred_unit:\n tag: preferred_unit\n value: mg/kg (ppm)\n occurrence:\n tag: occurrence\n value: '1'\ndescription: Concentration of zinc in the sample\ntitle: zinc\nexamples:\n- value: 2.5 mg/kg\nfrom_schema: https://w3id.org/nmdc/nmdc\nsee_also:\n- https://www.ornl.gov/content/bio-scales-0\naliases:\n- zinc\nrank: 1000\nalias: zinc\ndomain_of:\n- Biosample\nrange: QuantityValue\n\n