ERC000014 GSC MIxS human associated 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. ENA Organism characteristics: ecosystem trophic_level 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 optional single observed_biotic_relationship 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 optional single known_pathogenicity To what is the entity pathogenic, for instance plant, fungi, bacteria optional single relationship_to_oxygen 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 optional single propagation 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. optional single observed_host_symbionts The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. optional single sample collection: methods, storage and transport sample_collection_device 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). optional single sample_collection_method The method employed for collecting the sample. Can be provided in the form of a PMID, DOI, url or text. optional single urinecollection_method specification of urine collection method catheter clean catch optional single sample_storage_temperature temperature at which sample was stored, e.g. -80 [+-]?(0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? °C optional single sample_storage_location Location at which sample was stored, usually name of a specific freezer/room. Indicate the location name. optional single sample collection: core sample properties oxygenation_status_of_sample oxygenation status of sample aerobic anaerobic optional single medical_history_performed whether full medical history was collected No Yes optional single non-sample terms: study or project study_completion_status specification of study completion status, if no the reason should be specified No - adverse event No - lost to follow up No - non-compliance No - other Yes optional single project_name Name of the project within which the sequencing was organized mandatory single non-sample terms ploidy 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 optional single number_of_replicons 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. [+-]?[0-9]+ optional single extrachromosomal_elements Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids). [+-]?[0-9]+ optional single estimated_size 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. [+-]?[0-9]+ optional single target_gene Targeted gene or locus name for marker gene studies optional single target_subfragment Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA optional single multiplex_identifiers 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 optional single sequence_quality_check 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 optional single chimera_check_software 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. optional single relevant_electronic_resources A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a PMID, DOI or URL optional single relevant_standard_operating_procedures Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a PMID, DOI or URL optional single Collection event information collection_date 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. (^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$) mandatory single altitude The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air. ((0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)) m optional single geographic_location_latitude The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$) DD mandatory single geographic_location_longitude The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system (^[+-]?[0-9]+.?[0-9]{0,8}$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$) DD mandatory single geographic_location_region_and_locality The geographical origin of the sample as defined by the specific region name followed by the locality name. optional single broadscale_environmental_context 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. mandatory single local_environmental_context 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. mandatory single environmental_medium 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). mandatory single elevation The elevation of the sampling site as measured by the vertical distance from mean sea level. ([+-]?(0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)) m optional single sample collection amount_or_size_of_sample_collected The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. (0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? m2 m3 g L kg optional single organism_count Total 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) optional single Organism characteristics sample_storage_duration Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format. optional single geographic_location_country_andor_sea 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 Ecuador Egypt El Salvador Equatorial Guinea Eritrea Estonia Eswatini 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 Line Islands Lithuania Luxembourg Macau Madagascar Malawi Malaysia Maldives Mali Malta Marshall Islands Martinique Mauritania Mauritius Mayotte Mediterranean Sea Mexico Micronesia, Federated States of 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 Macedonia 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 Barthelemy Saint Helena Saint Kitts and Nevis Saint Lucia Saint Pierre and Miquelon Saint Vincent and the Grenadines Samoa San Marino Saint Martin 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 South Sudan Southern Ocean Spain Spratly Islands Sri Lanka State of Palestine Sudan Suriname Svalbard Sweden Switzerland Syria Taiwan Tajikistan Tanzania Tasman Sea Thailand Timor-Leste 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 Wake Island Virgin Islands 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 mandatory single host disorder nosemouthteeththroat_disorder History of nose/mouth/teeth/throat disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, nose disease (https://disease-ontology.org/?id=DOID:2825), mouth disease (https://disease-ontology.org/?id=DOID:403), tooth disease (https://disease-ontology.org/?id=DOID:1091), or upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). optional single host_hiv_status HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] No Yes optional single host_disease_status list 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 DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text optional single lungpulmonary_disorder History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). optional single lungnosethroat_disorder History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). optional single bloodblood_disorder History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). optional single urinekidney_disorder History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). optional single urineurogenital_tract_disorder History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). optional single host description host_subject_id a unique identifier by which each subject can be referred to, de-identified, e.g. #131 optional single ihmc_medication_code can include multiple medication codes 01=1=Analgesics/NSAIDS 02=2=Anesthetics 03=3=Antacids/H2 antagonists 04=4=Anti-acne 05=5=Anti-asthma/bronchodilators 06=6=Anti-cholesterol/Anti-hyperlipidemic 07=7=Anti-coagulants 08=8=Antibiotics/(anti)-infectives, parasitics, microbials 09=9=Antidepressants/mood-altering drugs 10=10=Antihistamines/ Decongestants 11=11=Antihypertensives 12=12=Cardiovascular, other than hyperlipidemic/HTN 13=13=Contraceptives (oral, implant, injectable) 14=14=Emergency/support medications 15=15=Endocrine/Metabolic agents 16=16=GI meds (anti-diarrheal, emetic, spasmodics) 17=17=Herbal/homeopathic products 18=18=Hormones/steroids 19=19=OTC cold & flu 20=20=Vaccine prophylaxis 21=21=Vitamins, minerals, food supplements 99=99=Other optional single host_age age 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 (0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? centuries hours seconds months weeks minutes days decades years optional single host_body_site name 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 3.1) terms, please see http://purl.bioontology.org/ontology/FMA optional single drug_usage any drug used by subject and the frequency of usage; can include multiple drugs used optional single host_height the height of subject ((0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)?)|((^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)) mm cm m optional single host_bodymass_index body mass index, calculated as weight/(height)squared (0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? kg/m2 optional single ethnicity A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups optional single host_occupation most frequent job performed by subject 01=01 Accounting/Finance 02=02 Advertising/Public Relations 03=03 Arts/Entertainment/Publishing 04=04 Automotive 05=05 Banking/ Mortgage 06=06 Biotech 07=07 Broadcast/Journalism 08=08 Business Development 09=09 Clerical/Administrative 10=10 Construction/Trades 11=11 Consultant 12=12 Customer Services 13=13 Design 14=14 Education 15=15 Engineering 16=16 Entry Level 17=17 Executive 18=18 Food Service 19=19 Government 20=20 Grocery 21=21 Healthcare 22=22 Hospitality 23=23 Human Resources 24=24 Information Technology 25=25 Insurance 26=26 Law/Legal 27=27 Management 28=28 Manufacturing 29=29 Marketing 30=30 Pharmaceutical 31=31 Professional Services 32=32 Purchasing 33=33 Quality Assurance (QA) 34=34 Research 35=35 Restaurant 36=36 Retail 37=37 Sales 38=38 Science 39=39 Security/Law Enforcement 40=40 Shipping/Distribution 41=41 Strategy 42=42 Student 43=43 Telecommunications 44=44 Training 45=45 Transportation 46=46 Warehouse 47=47 Other 99=99 Unknown/Refused optional single host_total_mass total mass of the host at collection, the unit depends on host (0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? g kg optional single host_phenotype phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO optional single host_body_temperature core body temperature of the host when sample was collected [+-]?(0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? ºC optional single host_sex Gender or sex of the host. female hermaphrodite male 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 neuter not applicable not collected not provided other restricted access optional single host_scientific_name Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained. optional single local environment conditions presence_of_pets_animals_or_insects The type and number of animals or insects present in the sampling space. optional single temperature temperature of the sample at time of sampling [+-]?(0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? ºC optional single concentration measurement salinity The 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. (0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? psu optional single Pointer to physical material source_material_identifiers A 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). optional single host details smoker specification of smoking status ex-smoker non-smoker smoker optional single major_diet_change_in_last_six_months specification of major diet changes in the last six months, if yes the change should be specified optional single weight_loss_in_last_three_months specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss g kg optional single travel_outside_the_country_in_last_six_months specification of the countries travelled in the last six months; can include multiple travels optional single host_diet type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, Mediterranean etc.; can include multiple diet types optional single twin_sibling_presence specification of twin sibling presence optional single host_last_meal content of last meal and time since feeding; can include multiple values optional single amniotic_fluidgestation_state specification of the gestation state optional single host_family_relationship Familial relationships to other hosts in the same study; can include multiple relationships optional single amniotic_fluidmaternal_health_status specification of the maternal health status optional single host_genotype observed genotype optional single amniotic_fluidfoetal_health_status specification of foetal health status, should also include abortion optional single host_pulse resting pulse, measured as beats per minute [+-]?[0-9]+ bpm optional single amniotic_fluidcolor specification of the color of the amniotic fluid sample optional single host_body_product substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA optional single treatment perturbation type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types optional single experimental factor and block negative_control_type The substance or equipment used as a negative control in an investigation optional single positive_control_type The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive. optional single experimental_factor Experimental 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. E.g. time series design [EFO:EFO_0001779] optional single Organism characteristics: genetic encoded_traits Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage optional single subspecific_genetic_lineage Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, 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. optional single taxonomic_classification Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes. Expected values are: classification method, database name, and other parameters e.g. vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters) optional single Reference isolation_and_growth_condition Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material. Mandatory for MIGS and MIMARKS Specimen. optional single annotation_source For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter optional single reference_for_biomaterial Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea. optional single sample processing sample_material_processing A 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. optional single sample_volume_or_weight_for_dna_extraction Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term 'sample size'. (0|((0\.)|([1-9][0-9]*\.?))[0-9]*)([Ee][+-]?[0-9]+)? g ng mg mL optional single nucleic_acid_extraction A 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 optional single nucleic_acid_amplification A 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 optional single library_size Total number of clones in the library prepared for the project [+-]?[0-9]+ optional single library_reads_sequenced Total number of clones sequenced from the library [+-]?[0-9]+ optional single library_construction_method Library construction method used for clone libraries optional single library_vector Cloning vector type(s) used in construction of libraries optional single library_screening_strategy Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences optional single pcr_conditions Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...' optional single pcr_primers PCR 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 optional single adapters Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters optional single local environment conditions imposed chemical_administration list 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) (v111), please see http://purl.bioontology.org/ontology/CHEBI optional single