Minimum information required for a prokaryotic pathogen sample
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. | |
| isolation_source | mandatory | Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived | |
| lat_lon | recommended | Geographical coordinates of the location where the specimen was collected | |
| collected_by | optional | Name of persons or institute who collected the specimen | |
| 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. | |
| geographic location (region and locality) | optional | The geographical origin of the sample as defined by the specific region name followed by the locality name. | |
| identified_by | optional | Name of the expert who identified the specimen taxonomically | |
| environmental_sample | optional | Identifies sequences derived by direct molecular isolation from a bulk environmental dna sample (by pcr with or without subsequent cloning of the product, dgge, or other anonymous methods) with no reliable identification of the source organism | No, Yes |
| mating_type | optional | Mating type of the organism from which the sequence was obtained; mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes | |
| geographic location (country and/or sea) | mandatory | The geographical origin of where the sample was collected from, with the intention of sequencing, as defined by the country or sea name. country or sea names should be chosen from the insdc country list (http://insdc.org/country.html). | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Arctic Ocean, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Atlantic Ocean, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Baltic Sea, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Czech Republic, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, East Timor, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indian Ocean, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Lithuania, Luxembourg, Macau, Macedonia, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mediterranean Sea, Mexico, Micronesia, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Sea, Northern Mariana Islands, Norway, Oman, Pacific Ocean, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Ross Sea, Russia, Rwanda, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, Southern Ocean, Spain, Spratly Islands, Sri Lanka, Sudan, Suriname, Svalbard, Swaziland, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Tasman Sea, Thailand, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, USA, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe, missing, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access |
| host health state | mandatory | Health status of the host at the time of sample collection. | diseased, healthy, missing: control sample, missing: data agreement established pre-2023, missing: endangered species, missing: human-identifiable, missing: lab stock, missing: sample group, missing: synthetic construct, missing: third party data, not applicable, not collected, not provided, restricted access |
| lab_host | optional | Scientific name of the laboratory host used to propagate the source organism from which the sample was obtained | |
| host scientific name | mandatory | Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained. | |
| bio_material | optional | Unique identifier that references the biological material from which the sample was obtained and that ideally exists in a curated collection (e.g. stock centres, seed banks, dna banks). the id should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). please note institution codes and collection codes are taken from a controlled vocabulary maintained by the insdc: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/ | |
| culture_collection | optional | Unique identifier that references the culture (e.g. live microbial and viral cultures and cell lines) from which the sample has been obtained and that have been deposited in curated culture collections. the id needs to provide an institution code and the culture id, with optional collection code, in the following structure: (-institution_code:(collection_code):voucher_id. please note institution codes (and optional collection codes) are taken from a controlled vocabulary maintained by the insdc: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/ | |
| specimen_voucher | optional | Unique identifier that references the physical specimen that remains after the sequence has been obtained and that ideally exists in a curated collection. the id should have the following structure: name of the institution (institution code) followed by the collection code (if available) and the voucher id (institution_code:collection_code:voucher_id). please note institution codes and collection codes are taken from a controlled vocabulary maintained by the insdc: https://ftp.ncbi.nih.gov/pub/taxonomy/biocollections/ | |
| isolate | mandatory | Individual isolate from which the sample was obtained | |
| sub_species | optional | Name of sub-species of organism from which sample was obtained | |
| sub_strain | optional | Name or identifier of a genetically or otherwise modified strain from which sample was obtained, derived from a parental strain (which should be annotated in the strain field; sub_strain from which sample was obtained | |
| serovar | recommended | Serological variety of a species (usually a prokaryote) characterized by its antigenic properties | |
| strain | recommended | Name of the strain from which the sample was obtained. |