ERC000055

ERC000055: GSC MIxS agriculture

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	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

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 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.
biotic relationship [deprecated]	recommended	Free text description of relationship(s) between the subject organism and other organism(s) it is associate 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
trophic level	recommended	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
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.
observed host symbionts	optional	The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.
sample collection device	optional	The device used to collect an environmental sample. it is recommended to use terms listed under environmental sampling device (http://purl.obolibrary.org/obo/envo) and/or terms listed under specimen collection device (http://purl.obolibrary.org/obo/genepio_0002094).
sample collection method	optional	The method employed for collecting the sample. can be provided in the form of a pmid, doi, url or text.
sample storage temperature	optional	Temperature at which sample was stored, e.g. -80 (Units: °C)
sample storage location	optional	Location at which sample was stored, usually name of a specific freezer/room. indicate the location name.
size-fraction lower threshold	optional	Refers to the mesh/pore size used to retain the sample. materials smaller than the size threshold are excluded from the sample (Units: µm)
size-fraction upper threshold	optional	Refers to the mesh/pore size used to pre-filter/pre-sort the sample. materials larger than the size threshold are excluded from the sample (Units: µm)
soil_taxonomic/FAO classification	recommended	Soil classification from the fao world reference database for soil resources
soil_taxonomic/local classification	recommended	Soil classification based on local soil classification system
soil_taxonomic/local classification method	recommended	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
soil pH	optional	Ph measurement of the soil; e.g. 6.2
soil cover	recommended	Description of the material covering the sampled soil. this field accepts terms under envo:00010483, environmental material.
oxygenation status of sample	recommended	Oxygenation status of sample	aerobic, anaerobic
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	optional	Name of the project within which the sequencing was organized
farm equipment sanitization	optional	Method used to sanitize growing and harvesting equipment. this can including type and concentration of sanitizing solution. multiple terms can be separated by one or more pipes.
equipment shared with other farms	optional	List of planting, growing or harvesting equipment shared with other farms. this field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/agro_00000416). multiple terms can be separated by pipes.
farm equipment used	optional	List of equipment used for planting, fertilization, harvesting, irrigation, land levelling, residue management, weeding or transplanting during the growing season. this field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/agro_00000416). multiple terms can be separated by pipes.
farm watering water source	recommended	Source of water used on the farm for irrigation of crops or watering of livestock.
food production system characteristics	optional	Descriptors of the food production system or of the agricultural environment and growing conditions related to the farm production system, such as wild caught, organic, free-range, industrial, dairy, beef, domestic or cultivated food production. this field accepts terms listed under food production (http://purl.obolibrary.org/obo/foodon_03530206). multiple terms may apply and can be separated by pipes.
animal water delivery method	optional	Description of the equipment or method used to distribute water to livestock. this field accepts termed listed under water delivery equipment (http://opendata.inra.fr/eol/eol_0001653). multiple terms can be separated by pipes.
plant water delivery method	recommended	Description of the equipment or method used to distribute water to crops. this field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/agro_00000006). multiple terms can be separated by pipes.
food harvesting process	optional	A harvesting process is a process which takes in some food material from an individual or community of plant or animal organisms in a given context and time, and outputs a precursor or consumable food product. this may include a part of an organism or the whole, and may involve killing the organism.
food production characteristics	optional	Descriptors of the food production system such as wild caught, free-range, organic, free-range, industrial, dairy, beef. (Units: °C)
fertilizer administration date	optional	Date of administration of soil amendment or fertilizer. multiple terms may apply and can be separated by pipes, listing in reverse chronological order.
crop yield	optional	Amount of crop produced per unit or area of land.
ploidy	optional	The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). it has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). for terms, please select terms listed under class ploidy (pato:001374) of phenotypic quality ontology (pato), and for a browser of pato (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/pato
number of replicons	optional	Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. always applied to the haploid chromosome count of a eukaryote. mandatory for migs of eukaryotes, bacteria, archaea and segmented virus.
extrachromosomal elements	optional	Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). megaplasmids? other plasmids (borrelia has 15+ plasmids).
estimated size	optional	The estimated size of the genome (in bp) prior to sequencing. of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period. mandatory for migs of eukaryotes.
target gene	optional	Targeted gene or locus name for marker gene studies
target subfragment	optional	Name of subfragment of a gene or locus. important to e.g. identify special regions on marker genes like v6 on 16s rrna
multiplex identifiers	optional	Molecular barcodes, called multiplex identifiers (mids), that are used to specifically tag unique samples in a sequencing run. sequence should be reported in uppercase letters
sequence quality check	optional	Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). applied only for sequences that are not submitted to sra or dra	manual, none, software
chimera check software	optional	Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. a chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.
relevant electronic resources	optional	A related resource that is referenced, cited, or otherwise associated to the sequence in the format of a pmid, doi or url
relevant standard operating procedures	optional	Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences in the format of a pmid, doi or url
16s recovered	optional	Can a 16s gene be recovered from the submitted bin, sag or mag?	No, Yes
16S recovery software	optional	Tools used for 16s rrna gene extraction. add names and versions of software(s), parameters used
collection date	mandatory	The date the sample was collected with the intention of sequencing, either as an instance (single point in time) or interval. in case no exact time is available, the date/time can be right truncated i.e. all of these are valid iso8601 compliant times: 2008-01-23t19:23:10+00:00; 2008-01-23t19:23:10; 2008-01-23; 2008-01; 2008.
altitude	optional	The altitude of the sample is the vertical distance between earth's surface above sea level and the sampled position in the air. (Units: m)
geographic location (latitude)	optional	The geographical origin of the sample as defined by latitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD)
geographic location (longitude)	optional	The geographical origin of the sample as defined by longitude. the values should be reported in decimal degrees and in wgs84 system (Units: DD)
geographic location (region and locality)	optional	The geographical origin of the sample as defined by the specific region name followed by the locality name.
broad-scale environmental context	optional	Report the major environmental system the sample or specimen came from. the system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). we recommend using subclasses of envo’s biome class: http://purl.obolibrary.org/obo/envo_00000428. envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs.
local environmental context	optional	Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. we recommend using envo terms which are of smaller spatial grain than your entry for "broad-scale environmental context". terms, such as anatomical sites, from other obo library ontologies which interoperate with envo (e.g. uberon) are accepted in this field. envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs.
environmental medium	optional	Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. we recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/envo_00010483). envo documentation about how to use the field: https://github.com/environmentontology/envo/wiki/using-envo-with-mixs . terms from other obo ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).
elevation	optional	The elevation of the sampling site as measured by the vertical distance from mean sea level. (Units: m)
culture isolation date	optional	A culture isolation date is a date-time entity marking the end of a process in which a sample yields a positive result for the target microbial analyte(s) in the form of an isolated colony or colonies.
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
organism count	recommended	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)
horizon method	recommended	Reference or method used in determining the horizon
extreme_unusual_properties/heavy metals	recommended	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	recommended	Reference or method used in determining heavy metals
plant structure	recommended	Name of plant structure that the sample was obtained from; for plant ontology (po) terms see http://purl.bioontology.org/ontology/po, e.g. petiole epidermis (po_0000051); if an individual flower is sampled the sex of it can be recorded here
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 disease status	recommended	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 common name	optional	Common name of the host, e.g. human
host age	optional	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 (Units: years)
host taxid	optional	Ncbi taxon id of the host, e.g. 9606
host life stage	optional	Description of life stage of host
host height	optional	The height of subject (Units: mm)
host length	optional	The length of subject (Units: mm)
host total mass	optional	Total mass of the host at collection, the unit depends on host (Units: kg)
host phenotype	optional	Phenotype of host. for phenotypic quality ontology (pato) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/pato
host scientific name	optional	Scientific name of the natural (as opposed to laboratory) host to the organism from which sample was obtained.
host subspecific genetic lineage	optional	Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, 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.
link to climate information	optional	Link to climate resource
link to classification information	optional	Link to digitized soil maps or other soil classification information
climate environment	recommended	Treatment involving an exposure to a particular climate; can include multiple climates
presence of pets, animals, or insects	optional	The type and number of animals or insects present in the sampling space.
current vegetation	recommended	Vegetation classification from one or more standard classification systems, or agricultural crop
gaseous environment	recommended	Use of conditions with differing gaseous environments; should include the name of gaseous compound, amount administered, treatment duration, interval and total experimental duration; can include multiple gaseous environment regimens
humidity	recommended	Amount of water vapour in the air, at the time of sampling (Units: g/m3)
current vegetation method	recommended	Reference or method used in vegetation classification
seasonal environment	recommended	Treatment involving an exposure to a particular season (e.g. winter, summer, rabi, rainy etc.)
soil horizon	recommended	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
solar irradiance	optional	The amount of solar energy that arrives at a specific area of a surface during a specific time interval (Units: W/m2)
drainage classification	recommended	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 method	recommended	Reference or method used in determining ph
slope gradient	recommended	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	recommended	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	recommended	Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas	backslope, footslope, shoulder, summit, toeslope
total organic carbon method	recommended	Reference or method used in determining total organic carbon
total nitrogen content method	recommended	Reference or method used in determining the total nitrogen
total phosphate	recommended	Total amount or concentration of phosphate (Units: µmol/L)
total nitrogen concentration	recommended	Concentration of nitrogen (total). total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. can also be measured without filtering, reported as nitrogen (Units: µmol/L)