Genomic Standards Consortium package extension for reporting of measurements and observations obtained from the environment where the sample was obtained. By choosing the environmental package, a selection of fields can be made from a relevant subsets of the GSC terms. This package is a combination of the four food extensions (MIxS-food-animal and animal feed, MIxS-food-farm environment, MIxS-food-food production facility, MIxS-food-human foods).
A Study is a container for a sequencing investigation that may comprise multiple experiments. The Study has an overall goal, but is otherwise minimally defined in the SRA. A Study is composed of a descriptor, zero or more experiments, and zero or more analyses. The submitter may decorate the Study with web links and properties.
| Field name | Cardinality | Description | Controlled vocabulary |
|---|---|---|---|
| alias | mandatory | Unique identificator for a study. this is used to link experiments to the study. | |
| title | mandatory | Title of the study as would be used in a publication. | |
| study_type | mandatory | The study_type presents a controlled vocabulary for expressing the overall purpose of the study. | Whole Genome Sequencing, Metagenomics, Transcriptome Analysis, Resequencing, Epigenetics, Synthetic Genomics, Forensic or Paleo-genomics, Gene Regulation Study, Cancer Genomics, Population Genomics, RNASeq, Exome Sequencing, Pooled Clone Sequencing, Transcriptome Sequencing, Other |
| new_study_type | optional | Optional if 'study_type' is not 'other'. to propose a new term, select other and enter a new study type. | |
| study_abstract | optional | Briefly describes the goals, purpose, and scope of the study. this need not be listed if it can be inherited from a referenced publication. |
An experiment object serves as a metadata record encapsulating essential details about a sequencing experiment, including the experimental design, sequencing type, and relevant parameters. This information enhances the interpretation and contextual understanding of nucleotide sequences submitted to the archive.
| Field name | Cardinality | Description | Controlled vocabulary |
|---|---|---|---|
| alias | mandatory | Unique identificator for each experiment. this is used to link runs to experiments. | |
| title | mandatory | Short text that can be used to call out experiment records in searches or in displays. this element is technically optional but should be used for all new records. | |
| study_alias | mandatory | Identifies the parent study. (from study metadata) | |
| sample_alias | mandatory | (from sample metadata) | |
| design_description | mandatory | Goal and setup of the individual library including library was constructed. | |
| library_name | optional | The submitter's name for this library. | |
| library_strategy | mandatory | Sequencing technique intended for this library. | WGS, WGA, WXS, RNA-Seq, ssRNA-seq, snRNA-seq, miRNA-Seq, ncRNA-Seq, FL-cDNA, EST, Hi-C, ATAC-seq, WCS, RAD-Seq, CLONE, POOLCLONE, AMPLICON, CLONEEND, FINISHING, ChIP-Seq, MNase-Seq, DNase-Hypersensitivity, Bisulfite-Seq, CTS, MRE-Seq, MeDIP-Seq, MBD-Seq, Tn-Seq, VALIDATION, FAIRE-seq, SELEX, RIP-Seq, ChIA-PET, Synthetic-Long-Read, Targeted-Capture, Tethered Chromatin Conformation Capture, NOMe-Seq, ChM-Seq, GBS, Ribo-Seq, OTHER |
| library_source | mandatory | The library_source specifies the type of source material that is being sequenced. | GENOMIC, GENOMIC SINGLE CELL, TRANSCRIPTOMIC, TRANSCRIPTOMIC SINGLE CELL, METAGENOMIC, METATRANSCRIPTOMIC, SYNTHETIC, VIRAL RNA, OTHER |
| library_selection | mandatory | Method used to enrich the target in the sequence library preparation | RANDOM, PCR, RANDOM PCR, RT-PCR, HMPR, MF, repeat fractionation, size fractionation, MSLL, cDNA, cDNA_randomPriming, cDNA_oligo_dT, PolyA, Oligo-dT, Inverse rRNA, Inverse rRNA selection, ChIP, ChIP-Seq, MNase, DNase, Hybrid Selection, Reduced Representation, Restriction Digest, 5-methylcytidine antibody, MBD2 protein methyl-CpG binding domain, CAGE, RACE, MDA, padlock probes capture method, other, unspecified |
| library_layout | mandatory | Library_layout specifies whether to expect single, paired, or other configuration of reads. in the case of paired reads, information about the relative distance and orientation is specified. | |
| insert_size | optional | Insert size for paired reads | |
| library_construction_protocol | optional | Free form text describing the protocol by which the sequencing library was constructed. | |
| platform | mandatory | The platform record selects which sequencing platform and platform-specific runtime parameters. this will be determined by the center. optional if 'instrument_model' is provided. | LS454, ILLUMINA, HELICOS, ABI_SOLID, COMPLETE_GENOMICS, BGISEQ, OXFORD_NANOPORE, PACBIO_SMRT, ION_TORRENT, CAPILLARY, DNBSEQ, ELEMENT, ULTIMA, VELA_DIAGNOSTICS, GENAPSYS, GENEMIND, TAPESTRI |
| instrument_model | mandatory | Model of the sequencing instrument. | 454 GS, 454 GS 20, 454 GS FLX, 454 GS FLX Titanium, 454 GS FLX+, 454 GS Junior, AB 310 Genetic Analyzer, AB 3130 Genetic Analyzer, AB 3130xL Genetic Analyzer, AB 3500 Genetic Analyzer, AB 3500xL Genetic Analyzer, AB 3730 Genetic Analyzer, AB 3730xL Genetic Analyzer, AB 5500 Genetic Analyzer, AB 5500xl Genetic Analyzer, AB 5500xl-W Genetic Analysis System, AB SOLiD 3 Plus System, AB SOLiD 4 System, AB SOLiD 4hq System, AB SOLiD PI System, AB SOLiD System, AB SOLiD System 2.0, AB SOLiD System 3.0, BGISEQ-50, BGISEQ-500, Complete Genomics, DNBSEQ-G400, DNBSEQ-G400 FAST, DNBSEQ-G50, DNBSEQ-T7, Element AVITI, FASTASeq 300, GENIUS, GS111, Genapsys Sequencer, GenoCare 1600, GenoLab M, GridION, Helicos HeliScope, HiSeq X Five, HiSeq X Ten, Illumina Genome Analyzer, Illumina Genome Analyzer II, Illumina Genome Analyzer IIx, Illumina HiScanSQ, Illumina HiSeq 1000, Illumina HiSeq 1500, Illumina HiSeq 2000, Illumina HiSeq 2500, Illumina HiSeq 3000, Illumina HiSeq 4000, Illumina HiSeq X, Illumina MiSeq, Illumina MiniSeq, Illumina NovaSeq 6000, Illumina NovaSeq X, Illumina iSeq 100, Ion GeneStudio S5, Ion GeneStudio S5 Plus, Ion GeneStudio S5 Prime, Ion Torrent Genexus, Ion Torrent PGM, Ion Torrent Proton, Ion Torrent S5, Ion Torrent S5 XL, MGISEQ-2000RS, MinION, NextSeq 1000, NextSeq 2000, NextSeq 500, NextSeq 550, Onso, PacBio RS, PacBio RS II, PromethION, Revio, Sentosa SQ301, Sequel, Sequel II, Sequel IIe, Tapestri, UG 100, unspecified |
A run contains a group of reads generated for a particular experiment.
| Field name | Cardinality | Description | Controlled vocabulary |
|---|---|---|---|
| alias | mandatory | Unique identificator for each run. | |
| experiment_alias | mandatory | From_experiment_metadata | |
| file_name | mandatory | The name or relative pathname of a run data file. | |
| file_format | mandatory | The run data file model. | sra, srf, sff, fastq, fasta, tab, 454_native, 454_native_seq, 454_native_qual, Helicos_native, Illumina_native, Illumina_native_seq, Illumina_native_prb, Illumina_native_int, Illumina_native_qseq, Illumina_native_scarf, SOLiD_native, SOLiD_native_csfasta, SOLiD_native_qual, PacBio_HDF5, bam, cram, CompleteGenomics_native, OxfordNanopore_native |
A Sample defines an isolate of sequenceable material upon which sequencing experiments can be based. The Sample object may be a surrogate for taxonomy accession or an anonymized individual identifier. Or, it may fully specify provenance and isolation method of the starting material.
| Field name | Cardinality | Description | Controlled vocabulary |
|---|---|---|---|
| alias | mandatory | Unique identificator for each sample. | |
| title | mandatory | Short text that can be used to call out sample records in search results or in displays. | |
| taxon_id | mandatory | Ncbi taxonomy identifier. this is appropriate for individual organisms and some environmental samples. | |
| sample_description | optional | Free-form text describing the sample, its origin, and its method of isolation. | |
| culture result | optional | Any result of a bacterial culture experiment reported as a binary assessment such as positive/negative, active/inactive. | |
| culture result organism | optional | Taxonomic information about the cultured organism(s). (Units: m2) | |
| culture target microbial analyte | optional | The target microbial analyte in terms of investigation scope. this field accepts terms under organism (http://purl.obolibrary.org/obo/ncit_c14250). this field also accepts identification numbers from ncbi under https://www.ncbi.nlm.nih.gov/taxonomy. | |
| biological sample replicate | optional | Measurements of biologically distinct samples that show biological variation. (Units: year) | |
| technical sample replicate | optional | Repeated measurements of the same sample that show independent measures of the noise associated with the equipment and the protocols. | |
| purpose of sampling | optional | The reason that the sample was collected. | |
| trophic level | optional | Trophic levels are the feeding position in a food chain. microbes can be a range of producers (e.g. chemolithotroph) | autotroph, carboxydotroph, chemoautotroph, chemoheterotroph, chemolithoautotroph, chemolithotroph, chemoorganoheterotroph, chemoorganotroph, chemosynthetic, chemotroph, copiotroph, diazotroph, facultative autotroph, heterotroph, lithoautotroph, lithoheterotroph, lithotroph, methanotroph, methylotroph, mixotroph, obligate chemoautolithotroph, oligotroph, organoheterotroph, organotroph, photoautotroph, photoheterotroph, photolithoautotroph, photolithotroph, photosynthetic, phototroph |
| observed biotic relationship | optional | Description 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. | commensal, free living, mutualism, parasite, symbiont |
| known pathogenicity | optional | To what is the entity pathogenic, for instance plant, fungi, bacteria | |
| relationship to oxygen | optional | Is this organism an aerobe, anaerobe? please note that aerobic and anaerobic are valid descriptors for microbial environments | aerobe, anaerobe, facultative, microaerophilic, microanaerobe, obligate aerobe, obligate anaerobe |
| propagation | optional | The type of reproduction from the parent stock. values for this field is specific to different taxa. for phage or virus: lytic/lysogenic/temperate/obligately lytic. for plasmids: incompatibility group. for eukaryotes: sexual/asexual. mandatory for migs of eukayotes, plasmids and viruses. | |
| sample transportation temperature | optional | Temperature at which sample was transported, e.g. -20 or 4 degree celsius. (Units: °C) | |
| sample transport container | optional | Container in which the sample was stored during transport. indicate the location name. (Units: J/°C) | |
| sample transport duration | optional | The duration of time from when the sample was collected until processed. indicate the duration for which the sample was stored written in iso 8601 format. (Units: year) | |
| sample collection device | optional | The device used to collect an environmental sample. it is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/envo) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/genepio_0002094). | |
| sample collection method | optional | The method employed for collecting the sample. can be provided in the form of a pmid, doi, url or text. | |
| sample storage temperature | optional | Temperature at which sample was stored, e.g. -80 (Units: °C) | |
| sample storage device | optional | The container used to store the sample. this field accepts terms listed under container (http://purl.obolibrary.org/obo/ncit_c43186). if the proper descriptor is not listed please use text to describe the storage device. | |
| sample storage location | optional | Location at which sample was stored, usually name of a specific freezer/room. indicate the location name. | |
| size-fraction lower threshold | optional | Refers to the mesh/pore size used to retain the sample. materials smaller than the size threshold are excluded from the sample (Units: µm) | |
| size-fraction upper threshold | optional | Refers to the mesh/pore size used to pre-filter/pre-sort the sample. materials larger than the size threshold are excluded from the sample (Units: µm) | |
| soil type | optional | Description 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. | Acrisol, Albeluvisol, Alisol, Andosol, Anthrosol, Arenosol, Calcisol, Cambisol, Chernozem, Cryosol, Durisol, Ferralsol, Fluvisol, Gleysol, Gypsisol, Histosol, Kastanozem, Leptosol, Lixisol, Luvisol, Nitisol, Phaeozem, Planosol, Plinthosol, Podzol, Regosol, Solonchak, Solonetz, Stagnosol, Technosol, Umbrisol, Vertisol |
| soil type method | optional | Reference or method used in determining soil series name or other lower-level classification | |
| soil texture method | optional | Reference or method used in determining soil texture | |
| soil pH | optional | Ph measurement of the soil; e.g. 6.2 | |
| soil cover | optional | Description of the material covering the sampled soil. this field accepts terms under envo:00010483, environmental material. | |
| soil texture classification | optional | One of the 12 soil texture classes use to describe soil texture based on the relative proportion of different grain sizes of mineral particles [sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um)] in a soil. (Units: °C) | |
| soil sediment porosity | optional | Porosity of soil or deposited sediment is volume of voids divided by the total volume of sample. | |
| soil conductivity | optional | Conductivity of soil at time of sampling. | |
| facility type | optional | Establishment details about the type of facility where the sample was taken. this is independent of the specific product(s) within the facility. | |
| collection site geographic feature | optional | Text or terms that describe the geographic feature where the food sample was obtained by the researcher. this field accepts selected terms listed under the following ontologies: anthropogenic geographic feature (http://purl.obolibrary.org/obo/envo_00000002), for example agricultural fairground [envo:01000986]; garden [envo:00000011} or any of its subclasses; market [envo:01000987]; water well [envo:01000002]; or human construction (http://purl.obolibrary.org/obo/envo_00000070). (Units: m2) | |
| area sampled size | optional | The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. (Units: ml) | |
| sample name | optional | Sample name is a name that you choose for the sample. it can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. every sample name from a single submitter must be unique. | |
| study design | optional | A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. this field accepts terms under study design (http://purl.obolibrary.org/obo/obi_0500000). if the proper descriptor is not listed please use text to describe the study design. multiple terms can be separated by pipes. (Units: kg s−3) | |
| project name | optional | Name of the project within which the sequencing was organized | |
| farm equipment sanitization | optional | Method used to sanitize growing and harvesting equipment. this can including type and concentration of sanitizing solution. multiple terms can be separated by one or more pipes. | |
| equipment shared with other farms | optional | List of planting, growing or harvesting equipment shared with other farms. this field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/agro_00000416). multiple terms can be separated by pipes. | |
| farm equipment used | optional | List of equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season. this field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/agro_00000416). multiple terms can be separated by pipes. | |
| farm equipment sanitization frequency | optional | The number of times farm equipment is cleaned. frequency of cleaning might be on a daily basis, weekly, monthly, quarterly or annually. (Units: m2) | |
| farm watering water source | optional | Source of water used on the farm for irrigation of crops or watering of livestock. | |
| food production system characteristics | optional | Descriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system, such as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated food production. this field accepts terms listed under food production (http://purl.obolibrary.org/obo/foodon_03530206). multiple terms may apply and can be separated by pipes. | |
| animal water delivery method | optional | Description of the equipment or method used to distribute water to livestock. this field accepts termed listed under water delivery equipment (http://opendata.inra.fr/eol/eol_0001653). multiple terms can be separated by pipes. | |
| plant water delivery method | optional | Description of the equipment or method used to distribute water to crops. this field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/agro_00000006). multiple terms can be separated by pipes. | |
| food harvesting process | optional | A harvesting process is a process which takes in some food material from an individual or community of plant or animal organisms in a given context and time, and outputs a precursor or consumable food product. this may include a part of an organism or the whole, and may involve killing the organism. | |
| food animal source diet | optional | If the isolate is from a food animal, the type of diet eaten by the food animal. please list the main food staple and the setting, if appropriate. for a list of acceptable animal feed terms or categories, please see http://www.feedipedia.org. multiple terms may apply and can be separated by pipes | food product for animal covers foods intended for consumption by domesticated animals. consult http://purl.obolibrary.org/obo/foodon_03309997. if the proper descriptor is not listed please use text to describe the food type. multiple terms can be separated by one or more pipes. if the proper descriptor is not listed please use text to describe the food product type. |
| food production characteristics | optional | Descriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, dairy, beef. (Units: °C) | |
| food animal group size | optional | The number of food animals of the same species that are maintained together as a unit, i.e. a herd or flock. (Units: year) | |
| fertilizer administration date | optional | Date of administration of soil amendment or fertilizer. multiple terms may apply and can be separated by pipes, listing in reverse chronological order. | |
| animal feeding equipment | optional | Description of the feeding equipment used for livestock. this field accepts terms listed under feed delivery (http://opendata.inra.fr/eol/eol_0001757). multiple terms can be separated by one or more pipes. | |
| crop yield | optional | Amount of crop produced per unit or area of land. | |
| water delivery frequency | optional | Number of water delivery events within a given period of time. | |
| animal housing system | optional | Description of the housing system of the livestock. this field accepts terms listed under terrestrial management housing system (http://opendata.inra.fr/eol/eol_0001605). | |
| environmental feature adjacent water source | optional | Description of the environmental features that are adjacent to the farm water source. this field accepts terms under ecosystem (http://purl.obolibrary.org/obo/envo_01001110) and human construction (http://purl.obolibrary.org/obo/envo_00000070). multiple terms can be separated by pipes. | |
| ploidy | optional | The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). it has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). for terms, please select terms listed under class ploidy (pato:001374) of phenotypic quality ontology (pato), and for a browser of pato (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/pato | |
| number of replicons | optional | Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. always applied to the haploid chromosome count of a eukaryote. mandatory for migs of eukaryotes, bacteria, archaea and segmented virus. | |
| extrachromosomal elements | optional | Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). megaplasmids? other plasmids (borrelia has 15+ plasmids). | |
| estimated size | optional | The estimated size of the genome (in bp) prior to sequencing. of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. mandatory for migs of eukaryotes. | |
| target gene | optional | Targeted gene or locus name for marker gene studies | |
| target subfragment | optional | Name of subfragment of a gene or locus. important to e.g. identify special regions on marker genes like v6 on 16s rrna | |
| multiplex identifiers | optional | Molecular barcodes, called multiplex identifiers (mids), that are used to specifically tag unique samples in a sequencing run. sequence should be reported in uppercase letters | |
| sequence quality check | optional | Indicate 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 or dra | manual, none, software |
| chimera check software | optional | Tool(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. | |
| relevant electronic resources | optional | A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a pmid, doi or url | |
| relevant standard operating procedures | optional | Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url | |
| 16s recovered | optional | Can a 16s gene be recovered from the submitted bin, sag or mag? | No, Yes |
| 16S recovery software | optional | Tools used for 16s rrna gene extraction. add names and versions of software(s), parameters used | |
| completeness score | optional | Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. completeness score is one of 3 attributes which in combination reflect the standard quality of a mag, see here for more information: https://ena-docs.readthedocs.io/en/latest/faq_metagenomes.html. mandatory for all samples directly linked with sags or mags. (Units: %) | |
| completeness software | optional | Tools used for completion estimate, i.e. checkm, anvi'o, busco. mandatory for all samples directly linked with sags or mags. | |
| completeness approach | optional | The approach used to determine the completeness of a given bin, sag or mag, which would typically make use of a set of conserved marker genes or a closely related reference genome. for uvig completeness, include reference genome or group used, and contig feature suggesting a complete genome | |
| assembly quality | optional | The assembly quality category is based on sets of criteria outlined for each assembly quality category. for misag/mimag; finished: single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to q50 or better. high quality draft:multiple fragments where gaps span repetitive regions. presence of the 23s, 16s and 5s rrna genes and at least 18 trnas. medium quality draft:many fragments with little to no review of assembly other than reporting of standard assembly statistics. low quality draft:many fragments with little to no review of assembly other than reporting of standard assembly statistics. assembly statistics include, but are not limited to total assembly size, number of contigs, contig n50/l50, and maximum contig length. for miuvig; finished: single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. high-quality draft genome: one or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. genome fragment(s): one or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated. | Many fragments with little to no review of assembly other than reporting of standard assembly statistics, Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs, Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better |
| assembly name | optional | Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community | |
| collection date | mandatory | The date the sample was collected with the intention of sequencing, 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 iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008. | |
| altitude | optional | The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m) | |
| geographic location (latitude) | optional | The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | |
| geographic location (longitude) | optional | The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD) | |
| geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | |
| broad-scale environmental context | optional | Report 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’s 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. | |
| local environmental context | optional | Report the entity or entities which are in the sample or specimen’s 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 "broad-scale environmental context". 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. | |
| environmental medium | optional | Report 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). | |
| elevation | optional | The elevation of the sampling site as measured by the vertical distance from mean sea level. (Units: m) | |
| culture isolation date | optional | A culture isolation date is a date-time entity marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies. | |
| time course duration | optional | For time-course research studies involving samples of the food commodity, indicate the total duration of the time-course study. (Units: year) | |
| number of samples collected | optional | The number of samples collected during the current sampling event. | |
| surface material | optional | Surface materials at the point of sampling | adobe, carpet, cinder blocks, concrete, glass, hay bales, metal, paint, plastic, stainless steel, stone, stucco, tile, vinyl, wood |
| ventilation rate | optional | Ventilation rate of the system in the sampled premises (Units: m3/min) | |
| indoor surface | optional | Type of indoor surface | cabinet, ceiling, counter top, door, shelving, vent cover, wall, window |
| ventilation type | optional | The intentional movement of air from outside a building to the inside through forced or natural movement of air | forced ventilation, mechanical ventilation, natural ventilation |
| sampling room sterilization method | optional | The method used to sterilize the sampling room. this field accepts terms listed under electromagnetic radiation (http://purl.obolibrary.org/obo/envo_01001026). if the proper descriptor is not listed, please use text to describe the sampling room sterilization method. multiple terms can be separated by pipes. | |
| sampling floor | optional | The floor of the building, where the sampling room is located (Units: °C) | |
| average daily occupancy | optional | Daily average occupancy of room. indicate the number of person(s) daily occupying the sampling room. (Units: °C) |