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.
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. | |
| number of inoculated individuals | optional | Number of host individuals inoculated for the experiment. | |
| 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 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. | |
| project name | mandatory | Name of the project within which the sequencing was organized | |
| frequency of cooking | optional | The number of times a meal is cooked per week | |
| 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 | |
| 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) | mandatory | 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) | mandatory | 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 | mandatory | 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 | mandatory | 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 | mandatory | 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) | |
| sampling time outside | optional | The recent and long term history of outside sampling | |
| temperature outside house | optional | The recorded temperature value at sampling time outside (Units: °C) | |
| train station collection location | optional | The train station collection location | |
| train stop collection location | optional | The train stop collection location | |
| 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 |
| surface-air contaminant | optional | Contaminant identified on surface | biocides, biological contaminants, dust, nutrients, organic matter, particulate matter, radon, volatile organic compounds |
| indoor surface | optional | Type of indoor surface | cabinet, ceiling, counter top, door, shelving, vent cover, wall, window |
| indoor space | mandatory | A distinguishable space within a structure, the purpose for which discrete areas of a building is used | bathroom, bedroom, elevator, foyer, hallway, kitchen, locker room, office |
| filter type | mandatory | A device which removes solid particulates or airborne molecular contaminants | HEPA filter, chemical air filter, electrostatic air treatment, gas-phase air treatment, low-MERV pleated media, particulate air filter, ultraviolet air treatment |
| heating and cooling system type | mandatory | Methods of conditioning or heating a room or building | forced air system, heat pump, radiant system, steam forced heat, wood stove |
| substructure type | optional | The substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level | basement, crawlspace, slab on grade |
| light type | mandatory | Application 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 | electric light, natural light, no light |
| building setting | mandatory | A location (geography) where a building is set | exurban, rural, suburban, urban |
| building occupancy type | mandatory | The primary function for which a building or discrete part of a building is intended to be used | agricultural, airport, commercial, educational, goverment, health care, high rise, industrial, low rise, market, military, office, parking, religious, residential, restaurant, school, sports complex, storage, transport, wood framed |
| space typical state | mandatory | Customary or normal state of the space | typically occupied, typically unoccupied |
| typical occupant density | mandatory | Customary or normal density of occupants | |
| occupancy at sampling | mandatory | Number of occupants present at time of sample within the given space | |
| occupant density at sampling | mandatory | Average number of occupants at time of sampling per square footage | |
| ventilation type | mandatory | 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 |
| rooms that are on the same hallway | optional | List of room(s) (room number, room name) located in the same hallway as sampling room | |
| wall surface treatment | optional | The surface treatment of interior wall | |
| wall area | optional | The total area of the sampled room's walls | |
| elevator count | optional | The number of elevators within the built structure | |
| floor area | optional | The area of the floor space within the room | |
| furniture | optional | The types of furniture present in the sampled room | |
| water feature type | optional | The type of water feature present within the building being sampled | |
| room door distance | optional | Distance between doors (meters) in the hallway between the sampling room and adjacent rooms | |
| room type | optional | The main purpose or activity of the sampling room. a room is any distinguishable space within a structure | |
| window location | optional | The relative location of the window within the room | |
| ceiling type | optional | The type of ceiling according to the ceiling's appearance or construction | |
| door direction of opening | optional | The direction the door opens | |
| exposed pipes | optional | The number of exposed pipes in the room | |
| wall height | optional | The average height of the walls in the sampled room | |
| door type, metal | optional | The type of metal door | |
| inside lux light | optional | The recorded value at sampling time (power density) (Units: kg s−3) | |
| exposed ductwork | optional | The amount of exposed ductwork in the room (Units: kg s−3) | |
| door material | optional | The material the door is composed of (Units: kg s−3) | |
| adjacent rooms | optional | List of rooms (room number, room name) immediately adjacent to the sampling room | |
| wall thermal mass | optional | The 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 (Units: J/°C) | |
| ceiling signs of water/mold | optional | Signs of the presence of mold or mildew on the ceiling (Units: J/°C) | |
| window status | optional | Defines whether the windows were open or closed during environmental testing (Units: %) | |
| door location | optional | The relative location of the door in the room (Units: year) | |
| window signs of water/mold | optional | Signs of the presence of mold or mildew on the window. (Units: year) | |
| window type | optional | The type of windows (Units: ppm) | |
| window material | optional | The type of material used to finish a window (Units: g/m3) | |
| window horizontal position | optional | The horizontal position of the window on the wall | |
| room condition | optional | The condition of the room at the time of sampling (Units: mm) | |
| window area/size | optional | The window's length and width (Units: mm) | |
| sampling floor | optional | The floor of the building, where the sampling room is located (Units: °C) | |
| room count | optional | The total count of rooms in the built structure including all room types | |
| average daily occupancy | optional | Daily average occupancy of room. indicate the number of person(s) daily occupying the sampling room. (Units: °C) | |
| floor condition | optional | The physical condition of the floor at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas (Units: °C) | |
| door type, wood | optional | The type of wood door (Units: °C) | |
| door condition | optional | The physical condition of the door | |
| door movement | optional | The type of movement of the door | |
| interior wall condition | optional | The physical condition of the wall at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas | |
| floor signs of water/mold | optional | Signs of the presence of mold or mildew in a room | |
| ceiling structure | optional | The construction format of the ceiling (Units: m) | |
| wall texture | optional | The feel, appearance, or consistency of a wall surface (Units: m) | |
| floor thermal mass | optional | The ability of the floor to provide inertia against temperature fluctuations (Units: J/°C) | |
| room air exchange rate | optional | The rate at which outside air replaces indoor air in a given space (Units: year) | |
| bathroom count | optional | The number of bathrooms in the building (Units: year) | |
| shading device signs of water/mold | optional | Signs of the presence of mold or mildew on the shading device (Units: year) | |
| window covering | optional | The type of window covering (Units: year) | |
| ceiling texture | optional | The feel, appearance, or consistency of a ceiling surface (Units: year) | |
| maximum occupancy | optional | The maximum amount of people allowed in the indoor environment (Units: year) | |
| gender of restroom | optional | The gender type of the restroom (Units: year) | |
| ceiling condition | optional | The physical condition of the ceiling at the time of sampling; photos or video preferred; use drawings to indicate location of damaged areas (Units: year) |