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ERC000024.json
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ERC000024.json
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{"id": "ERC000024", "dataTypeId": "samples", "displayName": "GSC MIxS water", "description": "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.", "spreadsheetTemplate": {"columnCaptures": {"alias": {"fieldName": "alias", "fieldType": "String", "required": true}, "title": {"fieldName": "title", "fieldType": "String", "required": true}, "description": {"fieldName": "description", "fieldType": "String", "required": false}, "release date": {"fieldName": "releaseDate", "required": true}, "taxon": {"fieldName": "taxon", "fieldType": "String", "required": true}, "taxon id": {"fieldName": "taxonId", "fieldType": "IntegerNumber", "required": true}, "project name": {"required": true, "allowUnits": false, "allowTerms": false}, "experimental factor": {"required": false, "allowUnits": false, "allowTerms": false}, "ploidy": {"required": false, "allowUnits": false, "allowTerms": false}, "number of replicons": {"required": false, "allowUnits": false, "allowTerms": false}, "extrachromosomal elements": {"required": false, "allowUnits": false, "allowTerms": false}, "estimated size": {"required": false, "allowUnits": false, "allowTerms": false}, "reference for biomaterial": {"required": false, "allowUnits": false, "allowTerms": false}, "finishing strategy": {"required": false, "allowUnits": false, "allowTerms": false}, "annotation source": {"required": false, "allowUnits": false, "allowTerms": false}, "sample volume or weight for DNA extraction": {"required": false, "allowUnits": false, "allowTerms": false}, "nucleic acid extraction": {"required": false, "allowUnits": false, "allowTerms": false}, "nucleic acid amplification": {"required": false, "allowUnits": false, "allowTerms": false}, "library size": {"required": false, "allowUnits": false, "allowTerms": false}, "library reads sequenced": {"required": false, "allowUnits": false, "allowTerms": false}, "library construction method": {"required": false, "allowUnits": false, "allowTerms": false}, "library vector": {"required": false, "allowUnits": false, "allowTerms": false}, "library screening strategy": {"required": false, "allowUnits": false, "allowTerms": false}, "target gene": {"required": false, "allowUnits": false, "allowTerms": false}, "target subfragment": {"required": false, "allowUnits": false, "allowTerms": false}, "pcr primers": {"required": false, "allowUnits": false, "allowTerms": false}, "multiplex identifiers": {"required": false, "allowUnits": false, "allowTerms": false}, "adapters": {"required": false, "allowUnits": false, "allowTerms": false}, "pcr conditions": {"required": false, "allowUnits": false, "allowTerms": false}, "sequencing method": {"required": true, "allowUnits": false, "allowTerms": false}, "sequence quality check": {"required": false, "allowUnits": false, "allowTerms": false}, "chimera check": {"required": false, "allowUnits": false, "allowTerms": false}, "relevant electronic resources": {"required": false, "allowUnits": false, "allowTerms": false}, "relevant standard operating procedures": {"required": false, "allowUnits": false, "allowTerms": false}, "investigation type": {"required": true, "allowUnits": false, "allowTerms": false}, "collection date": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (altitude)": {"required": false, "allowUnits": false, "allowTerms": false}, "geographic location (country and/or sea)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (latitude)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (longitude)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (region and locality)": {"required": false, "allowUnits": false, "allowTerms": false}, "water environmental package": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (depth)": {"required": true, "allowUnits": false, "allowTerms": false}, "environment (biome)": {"required": true, "allowUnits": false, "allowTerms": false}, "environment (feature)": {"required": true, "allowUnits": false, "allowTerms": false}, "environment (material)": {"required": true, "allowUnits": false, "allowTerms": false}, "geographic location (elevation)": {"required": false, "allowUnits": false, "allowTerms": false}, "source material identifiers": {"required": false, "allowUnits": false, "allowTerms": false}, "sample collection device or method": {"required": false, "allowUnits": false, "allowTerms": false}, "sample material processing": {"required": false, "allowUnits": false, "allowTerms": false}, "isolation and growth condition": {"required": false, "allowUnits": false, "allowTerms": false}, "propagation": {"required": false, "allowUnits": false, "allowTerms": false}, "amount or size of sample collected": {"required": false, "allowUnits": false, "allowTerms": false}, "biomass": {"required": false, "allowUnits": false, "allowTerms": false}, "density": {"required": false, "allowUnits": false, "allowTerms": false}, "oxygenation status of sample": {"required": false, "allowUnits": false, "allowTerms": false}, "organism count": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage duration": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage temperature": {"required": false, "allowUnits": false, "allowTerms": false}, "sample storage location": {"required": false, "allowUnits": false, "allowTerms": false}, "specific host": {"required": false, "allowUnits": false, "allowTerms": false}, "health or disease status of specific host": {"required": false, "allowUnits": false, "allowTerms": false}, "alkalinity": {"required": false, "allowUnits": false, "allowTerms": false}, "atmospheric data": {"required": false, "allowUnits": false, "allowTerms": false}, "conductivity": {"required": false, "allowUnits": false, "allowTerms": false}, "water current": {"required": false, "allowUnits": false, "allowTerms": false}, "fluorescence": {"required": false, "allowUnits": false, "allowTerms": false}, "light intensity": {"required": false, "allowUnits": false, "allowTerms": false}, "mean friction velocity": {"required": false, "allowUnits": false, "allowTerms": false}, "mean peak friction velocity": {"required": false, "allowUnits": false, "allowTerms": false}, "downward PAR": {"required": false, "allowUnits": false, "allowTerms": false}, "photon flux": {"required": false, "allowUnits": false, "allowTerms": false}, "pressure": {"required": false, "allowUnits": false, "allowTerms": false}, "temperature": {"required": false, "allowUnits": false, "allowTerms": false}, "tidal stage": {"required": false, "allowUnits": false, "allowTerms": false}, "pH": {"required": false, "allowUnits": false, "allowTerms": false}, "total depth of water column": {"required": false, "allowUnits": false, "allowTerms": false}, "alkyl diethers": {"required": false, "allowUnits": false, "allowTerms": false}, "aminopeptidase activity": {"required": false, "allowUnits": false, "allowTerms": false}, "ammonium": {"required": false, "allowUnits": false, "allowTerms": false}, "bacterial carbon production": {"required": false, "allowUnits": false, "allowTerms": false}, "bacterial production": {"required": false, "allowUnits": false, "allowTerms": false}, "bacterial respiration": {"required": false, "allowUnits": false, "allowTerms": false}, "bishomohopanol": {"required": false, "allowUnits": false, "allowTerms": false}, "bromide": {"required": false, "allowUnits": false, "allowTerms": false}, "calcium": {"required": false, "allowUnits": false, "allowTerms": false}, "carbon/nitrogen ratio": {"required": false, "allowUnits": false, "allowTerms": false}, "chloride": {"required": false, "allowUnits": false, "allowTerms": false}, "chlorophyll": {"required": false, "allowUnits": false, "allowTerms": false}, "diether lipids": {"required": false, "allowUnits": false, "allowTerms": false}, "dissolved carbon dioxide": {"required": false, "allowUnits": false, "allowTerms": false}, "dissolved hydrogen": {"required": false, "allowUnits": false, "allowTerms": false}, "dissolved inorganic carbon": {"required": false, "allowUnits": false, "allowTerms": false}, "dissolved inorganic nitrogen": {"required": false, "allowUnits": false, "allowTerms": false}, "dissolved inorganic phosphorus": {"required": false, "allowUnits": false, "allowTerms": false}, "dissolved organic carbon": {"required": false, "allowUnits": false, "allowTerms": false}, "dissolved organic nitrogen": {"required": false, "allowUnits": false, "allowTerms": false}, "dissolved oxygen": {"required": false, "allowUnits": false, "allowTerms": false}, "glucosidase activity": {"required": false, "allowUnits": false, "allowTerms": false}, "magnesium": {"required": false, "allowUnits": false, "allowTerms": false}, "n-alkanes": {"required": false, "allowUnits": false, "allowTerms": false}, "nitrate": {"required": false, "allowUnits": false, "allowTerms": false}, "nitrite": {"required": false, "allowUnits": false, "allowTerms": false}, "nitrogen": {"required": false, "allowUnits": false, "allowTerms": false}, "organic carbon": {"required": false, "allowUnits": false, "allowTerms": false}, "organic matter": {"required": false, "allowUnits": false, "allowTerms": false}, "organic nitrogen": {"required": false, "allowUnits": false, "allowTerms": false}, "particulate organic carbon": {"required": false, "allowUnits": false, "allowTerms": false}, "particulate organic nitrogen": {"required": false, "allowUnits": false, "allowTerms": false}, "petroleum hydrocarbon": {"required": false, "allowUnits": false, "allowTerms": false}, "phaeopigments": {"required": false, "allowUnits": false, "allowTerms": false}, "phosphate": {"required": false, "allowUnits": false, "allowTerms": false}, "phospholipid fatty acid": {"required": false, "allowUnits": false, "allowTerms": false}, "potassium": {"required": false, "allowUnits": false, "allowTerms": false}, "primary production": {"required": false, "allowUnits": false, "allowTerms": false}, "redox potential": {"required": false, "allowUnits": false, "allowTerms": false}, "salinity": {"required": false, "allowUnits": false, "allowTerms": false}, "silicate": {"required": false, "allowUnits": false, "allowTerms": false}, "sodium": {"required": false, "allowUnits": false, "allowTerms": false}, "soluble reactive phosphorus": {"required": false, "allowUnits": false, "allowTerms": false}, "sulfate": {"required": false, "allowUnits": false, "allowTerms": false}, "sulfide": {"required": false, "allowUnits": false, "allowTerms": false}, "suspended particulate matter": {"required": false, "allowUnits": false, "allowTerms": false}, "total dissolved nitrogen": {"required": false, "allowUnits": false, "allowTerms": false}, "total inorganic nitrogen": {"required": false, "allowUnits": false, "allowTerms": false}, "total nitrogen": {"required": false, "allowUnits": false, "allowTerms": false}, "total particulate carbon": {"required": false, "allowUnits": false, "allowTerms": false}, "total phosphorus": {"required": false, "allowUnits": false, "allowTerms": false}, "miscellaneous parameter": {"required": false, "allowUnits": false, "allowTerms": false}, "subspecific genetic lineage": {"required": false, "allowUnits": false, "allowTerms": false}, "trophic level": {"required": false, "allowUnits": false, "allowTerms": false}, "relationship to oxygen": {"required": false, "allowUnits": false, "allowTerms": false}, "known pathogenicity": {"required": false, "allowUnits": false, "allowTerms": false}, "encoded traits": {"required": false, "allowUnits": false, "allowTerms": false}, "observed biotic relationship": {"required": false, "allowUnits": false, "allowTerms": false}, "chemical administration": {"required": false, "allowUnits": false, "allowTerms": false}, "perturbation": {"required": false, "allowUnits": false, "allowTerms": false}}, "defaultCapture": {"required": false, "allowUnits": false, "allowTerms": false}}, "version": 1, "new": true, "validationSchema": {"version": "1.0.0", "author": "ENA", "definitions": {"attribute": {"type": "array", "minItems": 1, "items": {"required": ["value"], "properties": {"value": {"minLength": 1, "type": "string"}, "terms": {"$ref": "#/definitions/terms"}, "units": {"minLength": 1, "type": "string"}}}}, "terms": {"type": "array", "items": {"required": ["url"], "type": "object", "properties": {"url": {"format": "uri", "type": "string"}}}}, "properties": {"attributes": {"required": [], "type": "object", "description": "Attributes for describing a sample.", "patternProperties": {"^.*$": {"$ref": "#/definitions/attribute"}}, "properties": {}}}}, "description": "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.", "properties": {"attributes": {"required": ["project name", "sequencing method", "investigation type", "collection date", "geographic location (country and/or sea)", "geographic location (latitude)", "geographic location (longitude)", "water environmental package", "geographic location (depth)", "environment (biome)", "environment (feature)", "environment (material)"], "properties": {"light intensity": {"description": "measurement of light intensity", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "pressure": {"description": "pressure to which the sample is subject, in atmospheres", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "multiplex identifiers": {"description": "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", "items": {}}, "sodium": {"description": "sodium concentration", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "photon flux": {"description": "measurement of photon flux", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "organism count": {"description": "total count of any organism per gram or volume of sample, should include name of organism followed by count; can include multiple organism counts", "items": {}}, "library vector": {"description": "Cloning vector type(s) used in construction of libraries", "items": {}}, "library screening strategy": {"description": "Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences", "items": {}}, "oxygenation status of sample": {"description": "oxygenation status of sample", "items": {"properties": {"value": {"enum": ["aerobic", "anaerobic"]}}}}, "magnesium": {"description": "concentration of magnesium", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "observed biotic relationship": {"description": "Is it free-living or in a host and if the latter what type of relationship is observed", "items": {"properties": {"value": {"enum": ["commensal", "free living", "mutualism", "parasite", "symbiont"]}}}}, "sulfate": {"description": "concentration of sulfate", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "temperature": {"description": "temperature of the sample at time of sampling", "items": {"required": ["units"], "properties": {"value": {"pattern": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "source material identifiers": {"description": "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).", "items": {}}, "perturbation": {"description": "type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types", "items": {}}, "environment (biome)": {"description": "Biomes are defined based on factors such as plant structures, leaf types, plant spacing, and other factors like climate. Biome should be treated as the descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO", "items": {}}, "nitrate": {"description": "concentration of nitrate", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "environment (material)": {"description": "The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO", "items": {}}, "sequencing method": {"description": "Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid", "items": {}}, "geographic location (elevation)": {"description": "The elevation of the sampling site as measured by the vertical distance from mean sea level.", "items": {"required": ["units"], "properties": {"value": {"pattern": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "subspecific genetic lineage": {"description": "This should provide further information about the genetic distinctness of this lineage by recording additional information i.e biovar, serovar, serotype, biovar, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information", "items": {}}, "total dissolved nitrogen": {"description": "total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "redox potential": {"description": "redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "bishomohopanol": {"description": "concentration of bishomohopanol", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "phosphate": {"description": "concentration of phosphate", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "organic carbon": {"description": "concentration of organic carbon", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "relevant electronic resources": {"description": "-", "items": {}}, "miscellaneous parameter": {"description": "Any other measurement performed or parameter collected, that is not listed here", "items": {}}, "aminopeptidase activity": {"description": "measurement of aminopeptidase activity", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "total inorganic nitrogen": {"description": "total inorganic nitrogen content", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "nitrite": {"description": "concentration of nitrite", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "ammonium": {"description": "concentration of ammonium", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "chloride": {"description": "concentration of chloride", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "primary production": {"description": "measurement of primary production", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "experimental factor": {"description": "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 2.43) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI", "items": {}}, "investigation type": {"description": "Nucleic Acid Sequence Report is the root element of all MIxS compliant reports as standardised by Genomic Standards Consortium", "items": {"properties": {"value": {"enum": ["bacteria_archaea", "eukaryote", "metagenome", "metagenome-assembled genome", "metatranscriptome", "mimarks-specimen", "mimarks-survey", "organelle", "plasmid", "single amplified genome", "uncultivated viral genomes", "virus"]}}}}, "petroleum hydrocarbon": {"description": "concentration of petroleum hydrocarbon", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "target subfragment": {"description": "Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA", "items": {}}, "target gene": {"description": "Targeted gene or locus name for marker gene studies", "items": {}}, "conductivity": {"description": "electrical conductivity of water", "items": {"required": ["units"], "properties": {"value": {"pattern": "[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"}}}}, "amount or size of sample collected": {"description": "Amount or size of sample (volume, mass or area) that was collected", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "potassium": {"description": "concentration of potassium", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "trophic level": {"description": "Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)", "items": {"properties": {"value": {"enum": ["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"]}}}}, "diether lipids": {"description": "concentration of diether lipids; can include multiple types of diether lipids", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "phaeopigments": {"description": "concentration of phaeopigments; can include multiple phaeopigments", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sample volume or weight for DNA extraction": {"description": "Volume (mL) or weight (g) of sample processed for DNA extraction", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "environment (feature)": {"description": "Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO", "items": {}}, "carbon/nitrogen ratio": {"description": "ratio of amount or concentrations of carbon to nitrogen", "items": {"properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "chlorophyll": {"description": "concentration of chlorophyll", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "pH": {"description": "pH measurement", "items": {"properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "tidal stage": {"description": "stage of tide", "items": {"properties": {"value": {"enum": ["high", "low"]}}}}, "organic matter": {"description": "concentration of organic matter", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "dissolved carbon dioxide": {"description": "concentration of dissolved carbon dioxide", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "n-alkanes": {"description": "concentration of n-alkanes; can include multiple n-alkanes", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "dissolved organic carbon": {"description": "concentration of dissolved organic carbon", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "water current": {"description": "measurement of magnitude and direction of flow within a fluid", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "dissolved inorganic carbon": {"description": "dissolved inorganic carbon concentration", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sample storage duration": {"description": "duration for which sample was stored", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "total phosphorus": {"description": "total phosphorus concentration, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus. Can also be measured without filtering, reported as phosphorus", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "extrachromosomal elements": {"description": "Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids).", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "particulate organic carbon": {"description": "concentration of particulate organic carbon", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "nitrogen": {"description": "concentration of nitrogen (total)", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "total depth of water column": {"description": "measurement of total depth of water column", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "dissolved hydrogen": {"description": "concentration of dissolved hydrogen", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sample storage location": {"description": "location at which sample was stored, usually name of a specific freezer/room", "items": {}}, "atmospheric data": {"description": "measurement of atmospheric data; can include multiple data", "items": {}}, "dissolved inorganic phosphorus": {"description": "concentration of dissolved inorganic phosphorus", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "relationship to oxygen": {"description": "Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments", "items": {"properties": {"value": {"enum": ["aerobe", "anaerobe", "facultative", "microaerophilic", "microanaerobe", "obligate aerobe", "obligate anaerobe"]}}}}, "mean friction velocity": {"description": "measurement of mean friction velocity", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "bacterial respiration": {"description": "measurement of bacterial respiration in the water column", "items": {"required": ["units"], "properties": {"value": {"pattern": "[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"}}}}, "ploidy": {"description": "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 2013-10-28) please refer to http://purl.bioontology.org/ontology/PATO. Mandatory for MIGS of eukaryotes.", "items": {}}, "library reads sequenced": {"description": "Total number of clones sequenced from the library", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "chemical administration": {"description": "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", "items": {}}, "density": {"description": "density of sample", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "geographic location (country and/or sea)": {"description": "The geographical origin of the sample as defined by the country or sea. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html).", "items": {"properties": {"value": {"enum": ["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", "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", "not applicable", "not collected", "not provided", "restricted access"]}}}}, "known pathogenicity": {"description": "To what is the entity pathogenic, for instance plant, fungi, bacteria", "items": {}}, "dissolved organic nitrogen": {"description": "dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "total nitrogen": {"description": "total nitrogen content of the sample", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "adapters": {"description": "Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters", "items": {}}, "bromide": {"description": "concentration of bromide", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sample collection device or method": {"description": "The method or deviced employed for collecting the sample", "items": {}}, "bacterial production": {"description": "bacterial production in the water column measured by isotope uptake", "items": {"required": ["units"], "properties": {"value": {"pattern": "[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"}}}}, "dissolved inorganic nitrogen": {"description": "concentration of dissolved inorganic nitrogen", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "particulate organic nitrogen": {"description": "concentration of particulate organic nitrogen", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "pcr conditions": {"description": "Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'", "items": {}}, "geographic location (altitude)": {"description": "The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "collection date": {"description": "The date of sampling, 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.", "items": {"properties": {"value": {"pattern": "(^[0-9]{4}(-[0-9]{2}(-[0-9]{2}(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 collected$)|(^not provided$)|(^restricted access$)"}}}}, "project name": {"description": "Name of the project within which the sequencing was organized", "items": {}}, "propagation": {"description": "This field is specific to different taxa. For plants: sexual/asexual, for phages: lytic/lysogenic, for plasmids: incompatibility group (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice. Mandatory for MIGS of eukaryotes, plasmids and viruses.", "items": {}}, "sample storage temperature": {"description": "temperature at which sample was stored, e.g. -80", "items": {"required": ["units"], "properties": {"value": {"pattern": "[+-]?(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "nucleic acid amplification": {"description": "Link to a literature reference, electronic resource or a standard operating procedure (SOP)", "items": {}}, "alkalinity": {"description": "alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "phospholipid fatty acid": {"description": "concentration of phospholipid fatty acids; can include multiple values", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sulfide": {"description": "concentration of sulfide", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "organic nitrogen": {"description": "concentration of organic nitrogen", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "geographic location (depth)": {"description": "Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "glucosidase activity": {"description": "measurement of glucosidase activity", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "library size": {"description": "Total number of clones in the library prepared for the project", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "reference for biomaterial": {"description": "Primary publication if isolated before genome publication; otherwise, primary genome report. Mandatory for MIGS of bacteria and archaea.", "items": {}}, "library construction method": {"description": "Library construction method used for clone libraries", "items": {}}, "encoded traits": {"description": "Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage", "items": {}}, "isolation and growth condition": {"description": "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.", "items": {}}, "biomass": {"description": "amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements", "items": {"required": ["units"]}}, "geographic location (latitude)": {"description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", "items": {"required": ["units"], "properties": {"value": {"pattern": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "pcr primers": {"description": "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", "items": {}}, "fluorescence": {"description": "raw (volts) or converted (mg Chla/m^3) fluorescence of the water", "items": {"required": ["units"], "properties": {"value": {"pattern": "[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"}}}}, "annotation source": {"description": "For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter", "items": {}}, "calcium": {"description": "concentration of calcium", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "soluble reactive phosphorus": {"description": "concentration of soluble reactive phosphorus", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "sequence quality check": {"description": "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", "items": {"properties": {"value": {"enum": ["manual", "none", "software"]}}}}, "finishing strategy": {"description": "Was the genome project intended to produce a complete or draft genome, Coverage, the fold coverage of the sequencing expressed as 2x, 3x, 18x etc, and how many contigs were produced for the genome. Mandatory for MIGS of eukaryote, bacteria and archaea.", "items": {}}, "dissolved oxygen": {"description": "concentration of dissolved oxygen", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "chimera check": {"description": "A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point", "items": {}}, "number of replicons": {"description": "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.", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "water environmental package": {"description": "MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported", "items": {"properties": {"value": {"enum": ["water"]}}}}, "sample material processing": {"description": "Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI", "items": {}}, "suspended particulate matter": {"description": "concentration of suspended particulate matter", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "bacterial carbon production": {"description": "measurement of bacterial carbon production", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "silicate": {"description": "concentration of silicate", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "geographic location (longitude)": {"description": "The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system", "items": {"required": ["units"], "properties": {"value": {"pattern": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)"}}}}, "specific host": {"description": "If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host). From this we can calculate any number of groupings of hosts (e.g. animal vs plant, all fish hosts, etc)", "items": {}}, "estimated size": {"description": "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.", "items": {"properties": {"value": {"pattern": "[+-]?[0-9]+"}}}}, "relevant standard operating procedures": {"description": "Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences", "items": {}}, "health or disease status of specific host": {"description": "Health or disease status of specific host at time of collection. This field accepts PATO (v 2013-10-28) terms, for a browser please see http://purl.bioontology.org/ontology/PATO", "items": {}}, "salinity": {"description": "salinity measurement", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "geographic location (region and locality)": {"description": "The geographical origin of the sample as defined by the specific region name followed by the locality name.", "items": {}}, "mean peak friction velocity": {"description": "measurement of mean peak friction velocity", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "total particulate carbon": {"description": "total particulate carbon content", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "alkyl diethers": {"description": "concentration of alkyl diethers", "items": {"required": ["units"], "properties": {"value": {"pattern": "(0|((0\\.)|([1-9][0-9]*\\.?))[0-9]*)([Ee][+-]?[0-9]+)?"}}}}, "nucleic acid extraction": {"description": "Link to a literature reference, electronic resource or a standard operating procedure (SOP)", "items": {}}, "downward PAR": {"description": "visible waveband radiance and irradiance measurements in the water column", "items": {"required": ["units"], "properties": {"value": {"pattern": "[1-9][0-9]*\\.?[0-9]*([Ee][+-]?[0-9]+)?"}}}}}}}, "required": ["attributes"], "id": "ERC000024", "type": "object", "title": "GSC MIxS water", "$schema": "http://json-schema.org/draft-07/schema#", "$async": true}, "_links": {"self": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000024"}, "checklist": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000024"}, "spreadsheet-csv-download": {"href": "https://submission.ebi.ac.uk/api/checklists/ERC000024/spreadsheet.csv"}}}