ERC000022

ERC000022: GSC MIxS soil

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.

Study

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.

Experiment

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	optional	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	optional	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

Run

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

Sample

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 run.
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.
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.
sample storage conditions	optional	Conditions at which sample was stored, usually storage temperature, duration and location. in soil context: explain how and for how long the soil sample was stored before dna extraction (fresh/frozen/other).
soil_taxonomic/FAO classification	optional	Soil classification from the fao world reference database for soil resources
soil_taxonomic/local classification	optional	Soil classification based on local soil classification system
soil_taxonomic/local classification method	optional	Reference or method used in determining the local soil classification
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 measurement	optional	The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional. (Units: % sand/silt/clay)
soil texture method	optional	Reference or method used in determining soil texture
microbial biomass	optional	The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 µm. if you keep this, you would need to have correction factors used for conversion to the final units, which should be mg c (or n)/kg soil). (Units: g/kg)
project name	mandatory	Name of the project within which the sequencing was organized
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 (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: 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
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	mandatory	The elevation of the sampling site as measured by the vertical distance from mean sea level. (Units: m)
amount or size of sample collected	optional	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected. (Units: m3)
sieving	optional	Collection design of pooled samples and/or sieve size and amount of sample sieved
microbial biomass method	optional	Reference or method used in determining microbial biomass
horizon method	optional	Reference or method used in determining the horizon
extreme_unusual_properties/heavy metals	optional	Heavy metals present and concentrations of any drug used by subject and the frequency of usage; can include multiple heavy metals and concentrations
extreme_unusual_properties/heavy metals method	optional	Reference or method used in determining heavy metals
extreme_unusual_properties/Al saturation	optional	Aluminum saturation (esp. for tropical soils) (Units: %)
extreme_unusual_properties/Al saturation method	optional	Reference or method used in determining al saturation
host disease status	optional	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
host scientific name	optional	Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.
link to climate information	optional	Link to climate resource
link to classification information	optional	Link to digitized soil maps or other soil classification information
links to additional analysis	optional	Link to additional analysis results performed on the sample
current land use	optional	Present state of sample site
current vegetation	optional	Vegetation classification from one or more standard classification systems, or agricultural crop
current vegetation method	optional	Reference or method used in vegetation classification
soil horizon	optional	Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath	A horizon, B horizon, E horizon, O horizon, Permafrost, R layer
drainage classification	optional	Drainage classification from a standard system such as the usda system	excessively drained, moderately well, poorly, somewhat poorly, very poorly, well
temperature	optional	Temperature of the sample at time of sampling (Units: ºC)
pH	optional	Ph measurement
pH method	optional	Reference or method used in determining ph
water content	optional	Water content measurement e.g. soil water content of 13.6% (Units: g/g)
slope gradient	optional	Commonly called slope. the angle between ground surface and a horizontal line (in percent). this is the direction that overland water would flow. this measure is usually taken with a hand level meter or clinometer. (Units: %)
slope aspect	optional	The direction a slope faces. while looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315°. this measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration.
profile position	optional	Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas	backslope, footslope, shoulder, summit, toeslope
water content method	optional	Reference or method used in determining the water content of soil
total organic carbon method	optional	Reference or method used in determining total organic carbon
total nitrogen content method	optional	Reference or method used in determining the total nitrogen
organic matter	optional	Concentration of organic matter (Units: µg/L)
organic nitrogen	optional	Concentration of organic nitrogen (Units: µg/L)
total organic carbon	optional	Definition for soil: total organic c content of the soil units of g c/kg soil. definition otherwise: total organic carbon content (Units: g/kg)
total nitrogen content	optional	Total nitrogen content of the sample (Units: µmol/L)
salinity method	optional	Reference or method used in determining salinity
source material identifiers	optional	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).
history/previous land use	optional	Previous land use and dates
previous land use method	optional	Reference or method used in determining previous land use and dates
history/crop rotation	optional	Whether or not crop is rotated, and if yes, rotation schedule
history/agrochemical additions	optional	Addition of fertilizers, pesticides, etc. - amount and time of applications
history/tillage	optional	Note method(s) used for tilling	chisel, cutting disc, disc plough, drill, mouldboard, ridge till, strip tillage, tined, zonal tillage
history/fire	optional	Historical and/or physical evidence of fire
history/flooding	optional	Historical and/or physical evidence of flooding
history/extreme events	optional	Unusual physical events that may have affected microbial populations
mean seasonal temperature	optional	Mean seasonal temperature (Units: °C)
mean seasonal precipitation	optional	The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or isohyetal maps. (Units: mm)
mean annual precipitation	optional	The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or isohyetal maps. (Units: mm)
mean annual temperature	optional	Mean annual temperature (Units: ºC)
host specificity or range	optional	The range and diversity of host species that an organism is capable of infecting, defined by ncbi taxonomy identifier.
perturbation	optional	Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types
negative control type	optional	The substance or equipment used as a negative control in an investigation
positive control type	optional	The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive.
experimental factor	optional	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]
encoded traits	optional	Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage
subspecific genetic lineage	optional	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.
taxonomic classification	optional	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)
isolation and growth condition	optional	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.
annotation source	optional	For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
reference for biomaterial	optional	Primary publication if isolated before genome publication; otherwise, primary genome report. mandatory for migs of bacteria and archaea.
sample pooling	optional	Physical combination of several instances of like material, e.g. rna extracted from samples or dishes of cell cultures into one big aliquot of cells. please provide a short description of the samples that were pooled.
sample material processing	optional	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.
sample volume or weight for DNA extraction	optional	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'. (Units: ng)