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corneliusroemer/values.schema.json

Created January 27, 2025 12:18
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values.schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema#",
"additionalProperties": false,
"properties": {
"accessionPrefix": {
"default": "LOC_",
"required": [],
"title": "accessionPrefix",
"type": "string"
},
"additionalHeadHTML": {
"default": "",
"required": [],
"title": "additionalHeadHTML",
"type": "string"
},
"auth": {
"additionalProperties": false,
"properties": {
"identityProviders": {
"additionalProperties": false,
"properties": {
"orcid": {
"additionalProperties": false,
"properties": {
"clientId": {
"default": "APP-P1P7N7T9YVBHQ4EH",
"required": [],
"title": "clientId",
"type": "string"
}
},
"required": [
"clientId"
],
"title": "orcid",
"type": "object"
}
},
"required": [
"orcid"
],
"title": "identityProviders",
"type": "object"
},
"registrationAllowed": {
"default": true,
"required": [],
"title": "registrationAllowed",
"type": "boolean"
},
"resetPasswordAllowed": {
"default": true,
"required": [],
"title": "resetPasswordAllowed",
"type": "boolean"
},
"smtp": {
"additionalProperties": false,
"properties": {
"envelopeFrom": {
"default": "[email protected]",
"required": [],
"title": "envelopeFrom",
"type": "string"
},
"from": {
"default": "[email protected]",
"required": [],
"title": "from",
"type": "string"
},
"host": {
"default": "in-v3.mailjet.com",
"required": [],
"title": "host",
"type": "string"
},
"port": {
"default": 587,
"required": [],
"title": "port",
"type": "integer"
},
"replyTo": {
"default": "[email protected]",
"required": [],
"title": "replyTo",
"type": "string"
},
"user": {
"default": "fafd505de339dd2e9c3e85ad9981af8a",
"required": [],
"title": "user",
"type": "string"
}
},
"required": [
"host",
"port",
"user",
"replyTo",
"from",
"envelopeFrom"
],
"title": "smtp",
"type": "object"
},
"verifyEmail": {
"default": true,
"required": [],
"title": "verifyEmail",
"type": "boolean"
}
},
"required": [
"smtp",
"verifyEmail",
"resetPasswordAllowed",
"registrationAllowed",
"identityProviders"
],
"title": "auth",
"type": "object"
},
"bannerMessage": {
"default": "This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.",
"required": [],
"title": "bannerMessage",
"type": "string"
},
"dataUseTermsUrls": {
"additionalProperties": false,
"properties": {
"open": {
"default": "https://#TODO-MVP/open",
"required": [],
"title": "open",
"type": "string"
},
"restricted": {
"default": "https://#TODO-MVP/restricted",
"required": [],
"title": "restricted",
"type": "string"
}
},
"required": [
"open",
"restricted"
],
"title": "dataUseTermsUrls",
"type": "object"
},
"defaultOrganismConfig": {
"additionalProperties": false,
"properties": {
"enaDeposition": {
"additionalProperties": false,
"properties": {
"configFile": {
"additionalProperties": false,
"properties": {
"molecule_type": {
"default": "genomic RNA",
"required": [],
"title": "molecule_type",
"type": "string"
},
"scientific_name": {
"default": "Sudan ebolavirus",
"required": [],
"title": "scientific_name",
"type": "string"
},
"taxon_id": {
"default": 186540,
"required": [],
"title": "taxon_id",
"type": "integer"
}
},
"required": [
"taxon_id",
"scientific_name",
"molecule_type"
],
"title": "configFile",
"type": "object"
}
},
"required": [
"configFile"
],
"title": "enaDeposition",
"type": "object"
},
"ingest": {
"additionalProperties": false,
"properties": {
"configFile": {
"additionalProperties": false,
"properties": {
"taxon_id": {
"default": 186540,
"required": [],
"title": "taxon_id",
"type": "integer"
}
},
"required": [
"taxon_id"
],
"title": "configFile",
"type": "object"
},
"image": {
"default": "ghcr.io/loculus-project/ingest",
"required": [],
"title": "image",
"type": "string"
}
},
"required": [
"image",
"configFile"
],
"title": "ingest",
"type": "object"
},
"preprocessing": {
"items": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"args": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "args",
"type": "array"
},
"configFile": {
"additionalProperties": false,
"properties": {
"batch_size": {
"default": 100,
"required": [],
"title": "batch_size",
"type": "integer"
},
"genes": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "genes",
"type": "array"
},
"log_level": {
"default": "DEBUG",
"required": [],
"title": "log_level",
"type": "string"
},
"nextclade_dataset_name": {
"default": "nextstrain/ebola/sudan",
"required": [],
"title": "nextclade_dataset_name",
"type": "string"
}
},
"required": [
"log_level",
"nextclade_dataset_name",
"genes",
"batch_size"
],
"title": "configFile",
"type": "object"
},
"image": {
"default": "ghcr.io/loculus-project/preprocessing-nextclade",
"required": [],
"title": "image",
"type": "string"
},
"replicas": {
"default": 2,
"required": [],
"title": "replicas",
"type": "integer"
},
"version": {
"default": 1,
"required": [],
"title": "version",
"type": "integer"
}
},
"required": [
"version",
"image",
"args",
"replicas",
"configFile"
],
"type": "object"
}
],
"required": []
},
"required": [],
"title": "preprocessing",
"type": "array"
},
"referenceGenomes": {
"additionalProperties": false,
"properties": {
"genes": {
"items": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"name": {
"default": "NP",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/NP.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "VP35",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/VP35.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "VP40",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/VP40.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "GP",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/GP.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "ssGP",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/ssGP.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "sGP",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/sGP.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "VP30",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/VP30.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "VP24",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/VP24.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "L",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/L.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
}
],
"required": []
},
"required": [],
"title": "genes",
"type": "array"
},
"nucleotideSequences": {
"items": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"insdcAccessionFull": {
"default": "NC_002549.1",
"required": [],
"title": "insdcAccessionFull",
"type": "string"
},
"name": {
"default": "main",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/reference.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence",
"insdcAccessionFull"
],
"type": "object"
}
],
"required": []
},
"required": [],
"title": "nucleotideSequences",
"type": "array"
}
},
"required": [
"nucleotideSequences",
"genes"
],
"title": "referenceGenomes",
"type": "object"
},
"schema": {
"additionalProperties": false,
"properties": {
"earliestReleaseDate": {
"additionalProperties": false,
"properties": {
"enabled": {
"default": true,
"required": [],
"title": "enabled",
"type": "boolean"
},
"externalFields": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "externalFields",
"type": "array"
}
},
"required": [
"enabled",
"externalFields"
],
"title": "earliestReleaseDate",
"type": "object"
},
"extraInputFields": {
"items": {
"required": []
},
"required": [],
"title": "extraInputFields",
"type": "array"
},
"image": {
"default": "/images/organisms/ebolasudan_small.jpg",
"required": [],
"title": "image",
"type": "string"
},
"loadSequencesAutomatically": {
"default": true,
"required": [],
"title": "loadSequencesAutomatically",
"type": "boolean"
},
"metadata": {
"description": "# TODO: Allow extra metadata field by particular organisms (e.g. clade/lineage)",
"items": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"columnWidth": {
"default": 100,
"required": [],
"title": "columnWidth",
"type": "integer"
},
"displayName": {
"default": "Collection date",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiCollectionDate",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "sampleCollectionDate",
"required": [],
"title": "name",
"type": "string"
},
"notSearchable": {
"default": true,
"required": [],
"title": "notSearchable",
"type": "boolean"
},
"order": {
"default": 10,
"required": [],
"title": "order",
"type": "integer"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"fieldType": {
"default": "dateRangeString",
"required": [],
"title": "fieldType",
"type": "string"
}
},
"required": [
"fieldType"
],
"title": "args",
"type": "object"
},
"function": {
"default": "parse_date_into_range",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleCollectionDate",
"required": [],
"title": "date",
"type": "string"
},
"releaseDate": {
"default": "ncbiReleaseDate",
"required": [],
"title": "releaseDate",
"type": "string"
}
},
"required": [
"date",
"releaseDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"required": {
"default": true,
"required": [],
"title": "required",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"header",
"ingest",
"order",
"preprocessing",
"required",
"notSearchable",
"columnWidth"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Collection date (lower bound)",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "sampleCollectionDateRangeLower",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"fieldType": {
"default": "dateRangeLower",
"required": [],
"title": "fieldType",
"type": "string"
}
},
"required": [
"fieldType"
],
"title": "args",
"type": "object"
},
"function": {
"default": "parse_date_into_range",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleCollectionDate",
"required": [],
"title": "date",
"type": "string"
},
"releaseDate": {
"default": "ncbiReleaseDate",
"required": [],
"title": "releaseDate",
"type": "string"
}
},
"required": [
"date",
"releaseDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"rangeOverlapSearch": {
"additionalProperties": false,
"properties": {
"bound": {
"default": "lower",
"required": [],
"title": "bound",
"type": "string"
},
"rangeDisplayName": {
"default": "Collection date",
"required": [],
"title": "rangeDisplayName",
"type": "string"
},
"rangeName": {
"default": "sampleCollectionDateRange",
"required": [],
"title": "rangeName",
"type": "string"
}
},
"required": [
"rangeName",
"rangeDisplayName",
"bound"
],
"title": "rangeOverlapSearch",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"initiallyVisible",
"header",
"preprocessing",
"rangeOverlapSearch",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Collection date (upper bound)",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "sampleCollectionDateRangeUpper",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"fieldType": {
"default": "dateRangeUpper",
"required": [],
"title": "fieldType",
"type": "string"
}
},
"required": [
"fieldType"
],
"title": "args",
"type": "object"
},
"function": {
"default": "parse_date_into_range",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleCollectionDate",
"required": [],
"title": "date",
"type": "string"
},
"releaseDate": {
"default": "ncbiReleaseDate",
"required": [],
"title": "releaseDate",
"type": "string"
}
},
"required": [
"date",
"releaseDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"rangeOverlapSearch": {
"additionalProperties": false,
"properties": {
"bound": {
"default": "upper",
"required": [],
"title": "bound",
"type": "string"
},
"rangeDisplayName": {
"default": "Collection date",
"required": [],
"title": "rangeDisplayName",
"type": "string"
},
"rangeName": {
"default": "sampleCollectionDateRange",
"required": [],
"title": "rangeName",
"type": "string"
}
},
"required": [
"rangeName",
"rangeDisplayName",
"bound"
],
"title": "rangeOverlapSearch",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"initiallyVisible",
"header",
"preprocessing",
"rangeOverlapSearch",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "displayName",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"order": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "order",
"type": "array"
},
"type": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "type",
"type": "array"
}
},
"required": [
"order",
"type"
],
"title": "args",
"type": "object"
},
"function": {
"default": "concatenate",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"geoLocCountry": {
"default": "geoLocCountry",
"required": [],
"title": "geoLocCountry",
"type": "string"
},
"sampleCollectionDate": {
"default": "sampleCollectionDate",
"required": [],
"title": "sampleCollectionDate",
"type": "string"
}
},
"required": [
"geoLocCountry",
"sampleCollectionDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
}
},
"required": [
"name",
"preprocessing",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"columnWidth": {
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},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "options",
"type": "array"
}
},
"required": [
"options"
],
"title": "args",
"type": "object"
},
"function": {
"default": "process_options",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"input": {
"default": "geoLocCountry",
"required": [],
"title": "input",
"type": "string"
}
},
"required": [
"input"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"required": {
"default": true,
"required": [],
"title": "required",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"generateIndex",
"autocomplete",
"initiallyVisible",
"header",
"order",
"ingest",
"required",
"preprocessing"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"displayName": {
"default": "Collection subdivision level 1",
"required": [],
"title": "displayName",
"type": "string"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "division",
"required": [],
"title": "ingest",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "geoLocAdmin1",
"required": [],
"title": "name",
"type": "string"
},
"order": {
"default": 30,
"required": [],
"title": "order",
"type": "integer"
}
},
"required": [
"name",
"displayName",
"generateIndex",
"autocomplete",
"initiallyVisible",
"header",
"order",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"displayName": {
"default": "Collection subdivision level 2",
"required": [],
"title": "displayName",
"type": "string"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "geoLocAdmin2",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"generateIndex",
"autocomplete",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"displayName": {
"default": "Collection city",
"required": [],
"title": "displayName",
"type": "string"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "geoLocCity",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"generateIndex",
"autocomplete",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of a specific geographical location e.g. Credit River (rather than river).",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Collection site",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Credit River",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name of the specific geographical site using a specific noun (a word that names a certain place, thing).",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "geoLocSite",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100436",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Isolate name",
"required": [],
"title": "displayName",
"type": "string"
},
"enableSubstringSearch": {
"default": true,
"required": [],
"title": "enableSubstringSearch",
"type": "boolean"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiIsolateName",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "specimenCollectorSampleId",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header",
"ingest",
"enableSubstringSearch"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"columnWidth": {
"default": 140,
"required": [],
"title": "columnWidth",
"type": "integer"
},
"displayName": {
"default": "Authors",
"required": [],
"title": "displayName",
"type": "string"
},
"enableSubstringSearch": {
"default": true,
"required": [],
"title": "enableSubstringSearch",
"type": "boolean"
},
"header": {
"default": "Authors",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiSubmitterNames",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "authors",
"required": [],
"title": "name",
"type": "string"
},
"order": {
"default": 40,
"required": [],
"title": "order",
"type": "integer"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "check_authors",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"authors": {
"default": "authors",
"required": [],
"title": "authors",
"type": "string"
}
},
"required": [
"authors"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"truncateColumnDisplayTo": {
"default": 25,
"required": [],
"title": "truncateColumnDisplayTo",
"type": "integer"
},
"type": {
"default": "authors",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"header",
"enableSubstringSearch",
"order",
"truncateColumnDisplayTo",
"ingest",
"preprocessing",
"columnWidth"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Author affiliations",
"required": [],
"title": "displayName",
"type": "string"
},
"enableSubstringSearch": {
"default": true,
"required": [],
"title": "enableSubstringSearch",
"type": "boolean"
},
"header": {
"default": "Authors",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiSubmitterAffiliation",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "authorAffiliations",
"required": [],
"title": "name",
"type": "string"
},
"truncateColumnDisplayTo": {
"default": 15,
"required": [],
"title": "truncateColumnDisplayTo",
"type": "integer"
}
},
"required": [
"name",
"displayName",
"enableSubstringSearch",
"truncateColumnDisplayTo",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"displayName": {
"default": "NCBI submitter country",
"required": [],
"title": "displayName",
"type": "string"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "ncbiSubmitterCountry",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"generateIndex",
"autocomplete",
"hideOnSequenceDetailsPage",
"noInput",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "insdcAccessionBase",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
}
},
"required": [
"name",
"header",
"hideOnSequenceDetailsPage",
"noInput",
"perSegment",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "insdcVersion",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"header",
"hideOnSequenceDetailsPage",
"noInput",
"perSegment",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/nuccore/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"displayName": {
"default": "INSDC accession",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "genbankAccession",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "insdcAccessionFull",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
}
},
"required": [
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"displayName",
"customDisplay",
"header",
"ingest",
"noInput",
"perSegment",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/bioproject/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "bioprojects",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "bioprojectAccession",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
}
},
"required": [
"name",
"customDisplay",
"header",
"ingest",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/datasets/genome/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"displayName": {
"default": "GCA accession",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "gcaAccession",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"customDisplay",
"header",
"noInput",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/biosample/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "biosampleAccession",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
}
},
"required": [
"name",
"customDisplay",
"header",
"noInput",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Culture ID",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "cultureId",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The date on which the sample was received by the laboratory.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sample received date",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "2020-03-20",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Alternative if \"sampleCollectionDate\" is not available. Record the date the sample was received by the laboratory. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add \"jitter\" to the received date by adding or subtracting calendar days. Do not change the received date in your original records. Alternatively, collection_date may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\".",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sampleReceivedDate",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001177",
"required": [],
"title": "ontology_id",
"type": "string"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "parse_and_assert_past_date",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleReceivedDate",
"required": [],
"title": "date",
"type": "string"
}
},
"required": [
"date"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"preprocessing",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Sample type",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sampleType",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The reason that the sample was collected.",
"required": [],
"title": "definition",
"type": "string"
},
"example": {
"default": "Diagnostic testing",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select a value from the pick list in the template",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiPurposeOfSampling",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "purposeOfSampling",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001198",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The activities or variables introduced upstream of sample collection that may affect the sample collected.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Presampling activity",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Antimicrobial pre-treatment [GENEPIO:0100537]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If there was presampling activity that would affect the sample prior to collection (this is different than sample processing which happens after the sample is collected), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "presamplingActivity",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100433",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Anatomical material",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Blood [UBERON:0000178]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "anatomicalMaterial",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001211",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "An anatomical part of an organism e.g. oropharynx.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Anatomical part",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Nasopharynx (NP) [UBERON:0001728]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "anatomicalPart",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001214",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Body product",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Feces [UBERON:0001988]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "bodyProduct",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001216",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Environmental material",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Face mask [OBI:0002787]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "environmentalMaterial",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001223",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Environmental site",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Hospital [ENVO:00002173]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "environmentalSite",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001232",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The instrument or container used to collect the sample e.g. swab.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Collection device",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Swab [GENEPIO:0100027]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "collectionDevice",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001234",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The process used to collect the sample e.g. phlebotomy, necropsy.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Collection method",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Bronchoalveolar lavage (BAL) [GENEPIO:0100032]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "collectionMethod",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001241",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A material consumed and digested for nutritional value or enjoyment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Food product",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "foodProduct",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100444",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Food product properties",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free).",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "foodProductProperties",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100445",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Specimen processing",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Samples pooled [OBI:0600016]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Specimen processing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "specimenProcessing",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100435",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Detailed information regarding the processing applied to a sample during or after receiving the sample.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Specimen processing details",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "25 swabs were pooled and further prepared as a single sample during library prep.",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a free text description of any processing details applied to a sample.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Specimen processing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "specimenProcessingDetails",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100311",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The type of role that the sample represents in the experiment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Experimental specimen role type",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Positive experimental control [GENEPIO:0101018]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\".",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Specimen processing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "experimentalSpecimenRoleType",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100921",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Age of host at the time of sampling.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host age",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "79",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, provide age. Age-binning is also acceptable.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostAge",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001392",
"required": [],
"title": "ontology_id",
"type": "string"
},
"rangeSearch": {
"default": true,
"required": [],
"title": "rangeSearch",
"type": "boolean"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"header",
"rangeSearch"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The age category of the host at the time of sampling.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host age bin",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "50 - 59 [GENEPIO:0100054]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostAgeBin",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001394",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The gender of the host at the time of sample collection.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host gender",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Male [NCIT:C46109]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, select a value from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiHostSex",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "hostGender",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001395",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The country of origin of the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host origin country",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "South Africa [GAZ:00001094]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostOriginCountry",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100438",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the disease experienced by the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host disease",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "mastitis, gastroenteritis",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostDisease",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001391",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Signs and symptoms",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select all of the symptoms experienced by the host from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "signsAndSymptoms",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001400",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Health status of the host at the time of sample collection.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host health state",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Asymptomatic [NCIT:C3833]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, select a value from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostHealthState",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001388",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Disease outcome in the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host health outcome",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Recovered [NCIT:C49498]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, select a value from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostHealthOutcome",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001390",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Travel history in last six months.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Travel history",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Canada, Vancouver; USA, Seattle; Italy, Milan",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "travelHistory",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001416",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Event leading to exposure.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Exposure event",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Mass Gathering [GENEPIO:0100237]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, select the exposure event from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "exposureEvent",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001417",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The role of the host in relation to the exposure setting.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host role",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Patient [OMRSE:00000030]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostRole",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001419",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The setting leading to exposure.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Exposure setting",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Healthcare Setting [GENEPIO:0100201]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "exposureSetting",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001428",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Additional host exposure information.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Exposure details",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Host role - Other: Bus Driver",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Free text description of the exposure.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "exposureDetails",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001431",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the disease previously experienced by the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Previous infection (disease)",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "COVID-19",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name(s) of the previous of ongoing disease(s). Multiple diseases can be separated by a semi-colon.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "previousInfectionDisease",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the pathogen causing the disease previously experienced by the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Previous infection (organism)",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name(s) of the pathogen(s) causing the previous or ongoing infections. Multiple pathogen names can be separated using a semi-colon.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "previousInfectionOrganism",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host vaccination status",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Fully Vaccinated [GENEPIO:0100100]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select the vaccination status of the host from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostVaccinationStatus",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001404",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The reason that the sample was sequenced.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Purpose of sequencing",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Baseline surveillance (random sampling) [GENEPIO:0100005]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "purposeOfSequencing",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001445",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The date the sample was sequenced.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequencing date",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "2021-04-26",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the sequencing date in ISO 8601 standard format \"YYYY-MM-DD\".",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencingDate",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001447",
"required": [],
"title": "ontology_id",
"type": "string"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "parse_and_assert_past_date",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sequencingDate",
"required": [],
"title": "date",
"type": "string"
}
},
"required": [
"date"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"preprocessing",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Amplicon PCR primer scheme",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name and version of the primer scheme used to generate the amplicons for sequencing.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "ampliconPcrPrimerScheme",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001456",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The length of the amplicon generated by PCR amplification.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Amplicon size",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "300bp",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the amplicon size, including the units.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "ampliconSize",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001449",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The model of the sequencing instrument used.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequencing instrument",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Oxford Nanopore MinION [GENEPIO:0100142]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select the sequencing instrument from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencingInstrument",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001452",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The protocol used to generate the sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequencing protocol",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a tiling amplicon strategy using the \u003cfill in\u003e primer scheme. Sequencing was performed using a \u003cfill in\u003e sequencing instrument. Libraries were prepared using \u003cfill in\u003e library kit. \"",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencingProtocol",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001454",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequencing assay type",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "whole genome sequencing assay [OBI:0002117]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencingAssayType",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100997",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequenced by",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencedByOrganization",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100416",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name or title of the contact responsible for follow-up regarding the sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequenced by - contact name",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Enterics Lab Manager",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencedByContactName",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100471",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The email address of the contact responsible for follow-up regarding the sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequenced by - contact email",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "[email protected]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencedByContactEmail",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100422",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Raw sequence data processing method",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Porechop 0.2.3",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name and version numbers of the software used to process the raw data.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "rawSequenceDataProcessingMethod",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001458",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The method used to remove host reads from the pathogen sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Dehosting method",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Nanostripper 1.2.3",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name and version number of the software used to remove host reads.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "dehostingMethod",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001459",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A persistent, unique identifier of a genome database entry.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Reference genome accession",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "NC_045512.2",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the accession number of the reference genome used for mapping/assembly.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "referenceGenomeAccession",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001485",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of software used to generate the consensus sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Consensus sequence software name",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Ivar",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name of the software used to generate the consensus sequence.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "consensusSequenceSoftwareName",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001463",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The version of the software used to generate the consensus sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Consensus sequence software version",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "1.3",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the version of the software used to generate the consensus sequence.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "consensusSequenceSoftwareVersion",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001469",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The average number of reads representing a given nucleotide in the reconstructed sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Depth of coverage",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": 400,
"required": [],
"title": "example",
"type": "integer"
},
"guidance": {
"default": "Provide value as a fold of coverage (as a number).",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "depthOfCoverage",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001474",
"required": [],
"title": "ontology_id",
"type": "string"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The threshold used as a cut-off for the depth of coverage.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Breadth of coverage",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": 100,
"required": [],
"title": "example",
"type": "integer"
},
"guidance": {
"default": "Provide the threshold fold coverage (as a number)",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "breadthOfCoverage",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001475",
"required": [],
"title": "ontology_id",
"type": "string"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control method name",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "ncov-tools",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlMethodName",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100557",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control method version",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "1.2.3",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlMethodVersion",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100558",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The determination of a quality control assessment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control determination",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "sequence failed quality control",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlDetermination",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100559",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The reason contributing to, or causing, a low quality determination in a quality control assessment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control issues",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "low average genome coverage",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlIssues",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100560",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The details surrounding a low quality determination in a quality control assessment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control details",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "CT value of 39. Low viral load. Low DNA concentration after amplification.",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide notes or details regarding QC results using free text.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlDetails",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100561",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Diagnostic measurement method",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticMeasurementMethod",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Diagnostic target presence",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticTargetPresence",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Gene name",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticTargetGeneName",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Diagnostic measurement value",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticMeasurementValue",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Diagnostic measurement unit",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticMeasurementUnit",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Length",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Alignment states and QC metrics",
"required": [],
"title": "header",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "length",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
},
"rangeSearch": {
"default": true,
"required": [],
"title": "rangeSearch",
"type": "boolean"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"header",
"noInput",
"rangeSearch",
"initiallyVisible",
"perSegment",
"displayName"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiHostName",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "hostNameScientific",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"generateIndex",
"autocomplete",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiHostCommonName",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "hostNameCommon",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"generateIndex",
"autocomplete",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=info\u0026id=__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiHostTaxId",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "hostTaxonId",
"required": [],
"title": "name",
"type": "string"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"autocomplete",
"customDisplay",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiIsLabHost",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "isLabHost",
"required": [],
"title": "name",
"type": "string"
},
"type": {
"default": "boolean",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"autocomplete",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
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"type": "string"
}
],
"required": []
},
"required": [],
"title": "genes",
"type": "array"
},
"log_level": {
"default": "DEBUG",
"required": [],
"title": "log_level",
"type": "string"
},
"nextclade_dataset_name": {
"default": "nextstrain/ebola/sudan",
"required": [],
"title": "nextclade_dataset_name",
"type": "string"
}
},
"required": [
"log_level",
"nextclade_dataset_name",
"genes",
"batch_size"
],
"title": "configFile",
"type": "object"
},
"image": {
"default": "ghcr.io/loculus-project/preprocessing-nextclade",
"required": [],
"title": "image",
"type": "string"
},
"replicas": {
"default": 2,
"required": [],
"title": "replicas",
"type": "integer"
},
"version": {
"default": 1,
"required": [],
"title": "version",
"type": "integer"
}
},
"required": [
"version",
"image",
"args",
"replicas",
"configFile"
],
"type": "object"
}
],
"required": []
},
"required": [],
"title": "preprocessing",
"type": "array"
},
"referenceGenomes": {
"additionalProperties": false,
"properties": {
"genes": {
"items": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"name": {
"default": "NP",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/NP.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "VP35",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/VP35.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "VP40",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/VP40.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "GP",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/GP.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "ssGP",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/ssGP.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "sGP",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/sGP.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "VP30",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/VP30.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "VP24",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/VP24.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "L",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/L.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
}
],
"required": []
},
"required": [],
"title": "genes",
"type": "array"
},
"nucleotideSequences": {
"items": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"insdcAccessionFull": {
"default": "NC_002549.1",
"required": [],
"title": "insdcAccessionFull",
"type": "string"
},
"name": {
"default": "main",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/reference.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence",
"insdcAccessionFull"
],
"type": "object"
}
],
"required": []
},
"required": [],
"title": "nucleotideSequences",
"type": "array"
}
},
"required": [
"nucleotideSequences",
"genes"
],
"title": "referenceGenomes",
"type": "object"
},
"schema": {
"additionalProperties": false,
"properties": {
"earliestReleaseDate": {
"additionalProperties": false,
"properties": {
"enabled": {
"default": true,
"required": [],
"title": "enabled",
"type": "boolean"
},
"externalFields": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "externalFields",
"type": "array"
}
},
"required": [
"enabled",
"externalFields"
],
"title": "earliestReleaseDate",
"type": "object"
},
"extraInputFields": {
"items": {
"required": []
},
"required": [],
"title": "extraInputFields",
"type": "array"
},
"image": {
"default": "/images/organisms/ebolasudan_small.jpg",
"required": [],
"title": "image",
"type": "string"
},
"loadSequencesAutomatically": {
"default": true,
"required": [],
"title": "loadSequencesAutomatically",
"type": "boolean"
},
"metadata": {
"description": "# TODO: Allow extra metadata field by particular organisms (e.g. clade/lineage)",
"items": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"columnWidth": {
"default": 100,
"required": [],
"title": "columnWidth",
"type": "integer"
},
"displayName": {
"default": "Collection date",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiCollectionDate",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "sampleCollectionDate",
"required": [],
"title": "name",
"type": "string"
},
"notSearchable": {
"default": true,
"required": [],
"title": "notSearchable",
"type": "boolean"
},
"order": {
"default": 10,
"required": [],
"title": "order",
"type": "integer"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"fieldType": {
"default": "dateRangeString",
"required": [],
"title": "fieldType",
"type": "string"
}
},
"required": [
"fieldType"
],
"title": "args",
"type": "object"
},
"function": {
"default": "parse_date_into_range",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleCollectionDate",
"required": [],
"title": "date",
"type": "string"
},
"releaseDate": {
"default": "ncbiReleaseDate",
"required": [],
"title": "releaseDate",
"type": "string"
}
},
"required": [
"date",
"releaseDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"required": {
"default": true,
"required": [],
"title": "required",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"header",
"ingest",
"order",
"preprocessing",
"required",
"notSearchable",
"columnWidth"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Collection date (lower bound)",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "sampleCollectionDateRangeLower",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"fieldType": {
"default": "dateRangeLower",
"required": [],
"title": "fieldType",
"type": "string"
}
},
"required": [
"fieldType"
],
"title": "args",
"type": "object"
},
"function": {
"default": "parse_date_into_range",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleCollectionDate",
"required": [],
"title": "date",
"type": "string"
},
"releaseDate": {
"default": "ncbiReleaseDate",
"required": [],
"title": "releaseDate",
"type": "string"
}
},
"required": [
"date",
"releaseDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"rangeOverlapSearch": {
"additionalProperties": false,
"properties": {
"bound": {
"default": "lower",
"required": [],
"title": "bound",
"type": "string"
},
"rangeDisplayName": {
"default": "Collection date",
"required": [],
"title": "rangeDisplayName",
"type": "string"
},
"rangeName": {
"default": "sampleCollectionDateRange",
"required": [],
"title": "rangeName",
"type": "string"
}
},
"required": [
"rangeName",
"rangeDisplayName",
"bound"
],
"title": "rangeOverlapSearch",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"initiallyVisible",
"header",
"preprocessing",
"rangeOverlapSearch",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Collection date (upper bound)",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "sampleCollectionDateRangeUpper",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"fieldType": {
"default": "dateRangeUpper",
"required": [],
"title": "fieldType",
"type": "string"
}
},
"required": [
"fieldType"
],
"title": "args",
"type": "object"
},
"function": {
"default": "parse_date_into_range",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleCollectionDate",
"required": [],
"title": "date",
"type": "string"
},
"releaseDate": {
"default": "ncbiReleaseDate",
"required": [],
"title": "releaseDate",
"type": "string"
}
},
"required": [
"date",
"releaseDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"rangeOverlapSearch": {
"additionalProperties": false,
"properties": {
"bound": {
"default": "upper",
"required": [],
"title": "bound",
"type": "string"
},
"rangeDisplayName": {
"default": "Collection date",
"required": [],
"title": "rangeDisplayName",
"type": "string"
},
"rangeName": {
"default": "sampleCollectionDateRange",
"required": [],
"title": "rangeName",
"type": "string"
}
},
"required": [
"rangeName",
"rangeDisplayName",
"bound"
],
"title": "rangeOverlapSearch",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"initiallyVisible",
"header",
"preprocessing",
"rangeOverlapSearch",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "displayName",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"order": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "order",
"type": "array"
},
"type": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "type",
"type": "array"
}
},
"required": [
"order",
"type"
],
"title": "args",
"type": "object"
},
"function": {
"default": "concatenate",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"geoLocCountry": {
"default": "geoLocCountry",
"required": [],
"title": "geoLocCountry",
"type": "string"
},
"sampleCollectionDate": {
"default": "sampleCollectionDate",
"required": [],
"title": "sampleCollectionDate",
"type": "string"
}
},
"required": [
"geoLocCountry",
"sampleCollectionDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
}
},
"required": [
"name",
"preprocessing",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"columnWidth": {
"default": 100,
"required": [],
"title": "columnWidth",
"type": "integer"
},
"displayName": {
"default": "NCBI release date",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "ncbiReleaseDate",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "parse_timestamp",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"timestamp": {
"default": "ncbiReleaseDate",
"required": [],
"title": "timestamp",
"type": "string"
}
},
"required": [
"timestamp"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"header",
"preprocessing",
"noInput",
"columnWidth"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Earliest release date",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "earliestReleaseDate",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"rangeSearch": {
"default": true,
"required": [],
"title": "rangeSearch",
"type": "boolean"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header",
"type",
"rangeSearch",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"columnWidth": {
"default": 100,
"required": [],
"title": "columnWidth",
"type": "integer"
},
"displayName": {
"default": "NCBI update date",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "ncbiUpdateDate",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "parse_timestamp",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"timestamp": {
"default": "ncbiUpdateDate",
"required": [],
"title": "timestamp",
"type": "string"
}
},
"required": [
"timestamp"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"displayName",
"header",
"preprocessing",
"noInput",
"perSegment",
"oneHeader",
"columnWidth"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Latitude",
"required": [],
"title": "displayName",
"type": "string"
},
"guidance": {
"default": "Geo-coordinate latitude in decimal degree (WGS84) format, i.e. values in range -90 to 90, where positive values are north of the Equator.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "geoLocLatitude",
"required": [],
"title": "name",
"type": "string"
},
"type": {
"default": "float",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header",
"type",
"guidance"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Longitude",
"required": [],
"title": "displayName",
"type": "string"
},
"guidance": {
"default": "Geo-coordinate longitude in decimal degree (WGS84) format, i.e. values in range -180 to 180, where positive values are east of the Prime Meridian.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "geoLocLongitude",
"required": [],
"title": "name",
"type": "string"
},
"type": {
"default": "float",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header",
"type",
"guidance"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"displayName": {
"default": "Collection country",
"required": [],
"title": "displayName",
"type": "string"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
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"required": [
"name",
"displayName",
"header",
"ingest",
"enableSubstringSearch"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"columnWidth": {
"default": 140,
"required": [],
"title": "columnWidth",
"type": "integer"
},
"displayName": {
"default": "Authors",
"required": [],
"title": "displayName",
"type": "string"
},
"enableSubstringSearch": {
"default": true,
"required": [],
"title": "enableSubstringSearch",
"type": "boolean"
},
"header": {
"default": "Authors",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiSubmitterNames",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "authors",
"required": [],
"title": "name",
"type": "string"
},
"order": {
"default": 40,
"required": [],
"title": "order",
"type": "integer"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "check_authors",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"authors": {
"default": "authors",
"required": [],
"title": "authors",
"type": "string"
}
},
"required": [
"authors"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"truncateColumnDisplayTo": {
"default": 25,
"required": [],
"title": "truncateColumnDisplayTo",
"type": "integer"
},
"type": {
"default": "authors",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"header",
"enableSubstringSearch",
"order",
"truncateColumnDisplayTo",
"ingest",
"preprocessing",
"columnWidth"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Author affiliations",
"required": [],
"title": "displayName",
"type": "string"
},
"enableSubstringSearch": {
"default": true,
"required": [],
"title": "enableSubstringSearch",
"type": "boolean"
},
"header": {
"default": "Authors",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiSubmitterAffiliation",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "authorAffiliations",
"required": [],
"title": "name",
"type": "string"
},
"truncateColumnDisplayTo": {
"default": 15,
"required": [],
"title": "truncateColumnDisplayTo",
"type": "integer"
}
},
"required": [
"name",
"displayName",
"enableSubstringSearch",
"truncateColumnDisplayTo",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"displayName": {
"default": "NCBI submitter country",
"required": [],
"title": "displayName",
"type": "string"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "ncbiSubmitterCountry",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"generateIndex",
"autocomplete",
"hideOnSequenceDetailsPage",
"noInput",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "insdcAccessionBase",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
}
},
"required": [
"name",
"header",
"hideOnSequenceDetailsPage",
"noInput",
"perSegment",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "insdcVersion",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"header",
"hideOnSequenceDetailsPage",
"noInput",
"perSegment",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/nuccore/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"displayName": {
"default": "INSDC accession",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "genbankAccession",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "insdcAccessionFull",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"customDisplay",
"header",
"ingest",
"noInput",
"perSegment",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/bioproject/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "bioprojects",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "bioprojectAccession",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
}
},
"required": [
"name",
"customDisplay",
"header",
"ingest",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/datasets/genome/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"displayName": {
"default": "GCA accession",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "gcaAccession",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"customDisplay",
"header",
"noInput",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/biosample/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "biosampleAccession",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
}
},
"required": [
"name",
"customDisplay",
"header",
"noInput",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Culture ID",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "cultureId",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The date on which the sample was received by the laboratory.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sample received date",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "2020-03-20",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Alternative if \"sampleCollectionDate\" is not available. Record the date the sample was received by the laboratory. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add \"jitter\" to the received date by adding or subtracting calendar days. Do not change the received date in your original records. Alternatively, collection_date may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\".",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sampleReceivedDate",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001177",
"required": [],
"title": "ontology_id",
"type": "string"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "parse_and_assert_past_date",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleReceivedDate",
"required": [],
"title": "date",
"type": "string"
}
},
"required": [
"date"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"preprocessing",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Sample type",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sampleType",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The reason that the sample was collected.",
"required": [],
"title": "definition",
"type": "string"
},
"example": {
"default": "Diagnostic testing",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select a value from the pick list in the template",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiPurposeOfSampling",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "purposeOfSampling",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001198",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The activities or variables introduced upstream of sample collection that may affect the sample collected.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Presampling activity",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Antimicrobial pre-treatment [GENEPIO:0100537]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If there was presampling activity that would affect the sample prior to collection (this is different than sample processing which happens after the sample is collected), provide the experimental activities by selecting one or more values from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "presamplingActivity",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100433",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A substance obtained from an anatomical part of an organism e.g. tissue, blood.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Anatomical material",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Blood [UBERON:0000178]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if an anatomical material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "anatomicalMaterial",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001211",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "An anatomical part of an organism e.g. oropharynx.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Anatomical part",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Nasopharynx (NP) [UBERON:0001728]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if an anatomical part was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "anatomicalPart",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001214",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A substance excreted/secreted from an organism e.g. feces, urine, sweat.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Body product",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Feces [UBERON:0001988]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if a body product was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/uberon. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "bodyProduct",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001216",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Environmental material",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Face mask [OBI:0002787]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if an environmental material was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "environmentalMaterial",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001223",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Environmental site",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Hospital [ENVO:00002173]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if an environmental site was sampled. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/envo. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "environmentalSite",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001232",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The instrument or container used to collect the sample e.g. swab.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Collection device",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Swab [GENEPIO:0100027]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if a collection device was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "collectionDevice",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001234",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The process used to collect the sample e.g. phlebotomy, necropsy.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Collection method",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Bronchoalveolar lavage (BAL) [GENEPIO:0100032]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a descriptor if a collection method was used for sampling. Use the pick list provided in the template. If a desired term is missing from the pick list, use this look-up service to identify a standardized term: https://www.ebi.ac.uk/ols/ontologies/obi. If not applicable, leave blank.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "collectionMethod",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001241",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A material consumed and digested for nutritional value or enjoyment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Food product",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "foodProduct",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100444",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Food product properties",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free).",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sampling",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "foodProductProperties",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100445",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Specimen processing",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Samples pooled [OBI:0600016]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Specimen processing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "specimenProcessing",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100435",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Detailed information regarding the processing applied to a sample during or after receiving the sample.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Specimen processing details",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "25 swabs were pooled and further prepared as a single sample during library prep.",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a free text description of any processing details applied to a sample.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Specimen processing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "specimenProcessingDetails",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100311",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The type of role that the sample represents in the experiment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Experimental specimen role type",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Positive experimental control [GENEPIO:0101018]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select \"Not Applicable\".",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Specimen processing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "experimentalSpecimenRoleType",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100921",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Age of host at the time of sampling.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host age",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "79",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, provide age. Age-binning is also acceptable.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostAge",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001392",
"required": [],
"title": "ontology_id",
"type": "string"
},
"rangeSearch": {
"default": true,
"required": [],
"title": "rangeSearch",
"type": "boolean"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"header",
"rangeSearch"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The age category of the host at the time of sampling.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host age bin",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "50 - 59 [GENEPIO:0100054]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostAgeBin",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001394",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The gender of the host at the time of sample collection.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host gender",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Male [NCIT:C46109]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, select a value from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiHostSex",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "hostGender",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001395",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The country of origin of the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host origin country",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "South Africa [GAZ:00001094]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostOriginCountry",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100438",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the disease experienced by the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host disease",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "mastitis, gastroenteritis",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "This field is only required if the Pathogen.cl package was selected. If the host was sick, provide the name of the disease.The standardized term can be sourced from this look-up service: https://www.ebi.ac.uk/ols/ontologies/doid If the disease is not known, put “missing”.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostDisease",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001391",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Signs and symptoms",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Cough [HP:0012735], Fever [HP:0001945], Rigors (fever shakes) [HP:0025145]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select all of the symptoms experienced by the host from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "signsAndSymptoms",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001400",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Health status of the host at the time of sample collection.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host health state",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Asymptomatic [NCIT:C3833]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, select a value from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostHealthState",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001388",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Disease outcome in the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host health outcome",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Recovered [NCIT:C49498]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, select a value from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostHealthOutcome",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001390",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Travel history in last six months.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Travel history",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Canada, Vancouver; USA, Seattle; Italy, Milan",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "travelHistory",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001416",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Event leading to exposure.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Exposure event",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Mass Gathering [GENEPIO:0100237]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "If known, select the exposure event from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "exposureEvent",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001417",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The role of the host in relation to the exposure setting.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host role",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Patient [OMRSE:00000030]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select the host's personal role(s) from the pick list provided in the template. If the desired term is missing, contact the curation team.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostRole",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001419",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The setting leading to exposure.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Exposure setting",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Healthcare Setting [GENEPIO:0100201]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select the host exposure setting(s) from the pick list provided in the template. If a desired term is missing, contact the curation team.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "exposureSetting",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001428",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "Additional host exposure information.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Exposure details",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Host role - Other: Bus Driver",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Free text description of the exposure.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "exposureDetails",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001431",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the disease previously experienced by the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Previous infection (disease)",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "COVID-19",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name(s) of the previous of ongoing disease(s). Multiple diseases can be separated by a semi-colon.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "previousInfectionDisease",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the pathogen causing the disease previously experienced by the host.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Previous infection (organism)",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name(s) of the pathogen(s) causing the previous or ongoing infections. Multiple pathogen names can be separated using a semi-colon.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "previousInfectionOrganism",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Host vaccination status",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Fully Vaccinated [GENEPIO:0100100]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select the vaccination status of the host from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "hostVaccinationStatus",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001404",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The reason that the sample was sequenced.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Purpose of sequencing",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Baseline surveillance (random sampling) [GENEPIO:0100005]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the \"purpose of sampling\" field.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "purposeOfSequencing",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001445",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The date the sample was sequenced.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequencing date",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "2021-04-26",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the sequencing date in ISO 8601 standard format \"YYYY-MM-DD\".",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencingDate",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001447",
"required": [],
"title": "ontology_id",
"type": "string"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "parse_and_assert_past_date",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sequencingDate",
"required": [],
"title": "date",
"type": "string"
}
},
"required": [
"date"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"preprocessing",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Amplicon PCR primer scheme",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "https://github.com/joshquick/artic-ncov2019/blob/master/primer_schemes/nCoV-2019/V3/nCoV-2019.tsv",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name and version of the primer scheme used to generate the amplicons for sequencing.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "ampliconPcrPrimerScheme",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001456",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The length of the amplicon generated by PCR amplification.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Amplicon size",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "300bp",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the amplicon size, including the units.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "ampliconSize",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001449",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The model of the sequencing instrument used.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequencing instrument",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Oxford Nanopore MinION [GENEPIO:0100142]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select the sequencing instrument from the pick list.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencingInstrument",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001452",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The protocol used to generate the sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequencing protocol",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Genomes were generated through amplicon sequencing of 1200 bp amplicons with Freed schema primers. Libraries were created using Illumina DNA Prep kits, and sequence data was produced using Miseq Micro v2 (500 cycles) sequencing kits.",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide a free text description of the methods and materials used to generate the sequence. Suggested text, fill in information where indicated.: \"Viral sequencing was performed following a tiling amplicon strategy using the \u003cfill in\u003e primer scheme. Sequencing was performed using a \u003cfill in\u003e sequencing instrument. Libraries were prepared using \u003cfill in\u003e library kit. \"",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencingProtocol",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001454",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The overarching sequencing methodology that was used to determine the sequence of a biomaterial.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequencing assay type",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "whole genome sequencing assay [OBI:0002117]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencingAssayType",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100997",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the agency, organization or institution responsible for sequencing the isolate's genome.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequenced by",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Public Health Agency of Canada (PHAC) [GENEPIO:0100551]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencedByOrganization",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100416",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name or title of the contact responsible for follow-up regarding the sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequenced by - contact name",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Enterics Lab Manager",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more preferable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencedByContactName",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100471",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The email address of the contact responsible for follow-up regarding the sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sequenced by - contact email",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "[email protected]",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more preferable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "sequencedByContactEmail",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100422",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Raw sequence data processing method",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Porechop 0.2.3",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name and version numbers of the software used to process the raw data.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "rawSequenceDataProcessingMethod",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001458",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The method used to remove host reads from the pathogen sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Dehosting method",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Nanostripper 1.2.3",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name and version number of the software used to remove host reads.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "dehostingMethod",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001459",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "A persistent, unique identifier of a genome database entry.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Reference genome accession",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "NC_045512.2",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the accession number of the reference genome used for mapping/assembly.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "referenceGenomeAccession",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001485",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of software used to generate the consensus sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Consensus sequence software name",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "Ivar",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the name of the software used to generate the consensus sequence.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "consensusSequenceSoftwareName",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001463",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The version of the software used to generate the consensus sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Consensus sequence software version",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "1.3",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide the version of the software used to generate the consensus sequence.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "consensusSequenceSoftwareVersion",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001469",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The average number of reads representing a given nucleotide in the reconstructed sequence.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Depth of coverage",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": 400,
"required": [],
"title": "example",
"type": "integer"
},
"guidance": {
"default": "Provide value as a fold of coverage (as a number).",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "depthOfCoverage",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001474",
"required": [],
"title": "ontology_id",
"type": "string"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The threshold used as a cut-off for the depth of coverage.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Breadth of coverage",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": 100,
"required": [],
"title": "example",
"type": "integer"
},
"guidance": {
"default": "Provide the threshold fold coverage (as a number)",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "breadthOfCoverage",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0001475",
"required": [],
"title": "ontology_id",
"type": "string"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"type",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The name of the method used to assess whether a sequence passed a predetermined quality control threshold.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control method name",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "ncov-tools",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Providing the name of the method used for quality control is very important for interpreting the rest of the QC information. Method names can be provided as the name of a pipeline or a link to a GitHub repository. Multiple methods should be listed and separated by a semi-colon. Do not include QC tags in other fields if no method name is provided.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlMethodName",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100557",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The version number of the method used to assess whether a sequence passed a predetermined quality control threshold.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control method version",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "1.2.3",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Methods updates can make big differences to their outputs. Provide the version of the method used for quality control. The version can be expressed using whatever convention the developer implements (e.g. date, semantic versioning). If multiple methods were used, record the version numbers in the same order as the method names. Separate the version numbers using a semi-colon.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlMethodVersion",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100558",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The determination of a quality control assessment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control determination",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "sequence failed quality control",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlDetermination",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100559",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The reason contributing to, or causing, a low quality determination in a quality control assessment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control issues",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "low average genome coverage",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Select a value from the pick list provided. If a desired value is missing, submit a new term request to the PHA4GE QC Tag GitHub issuetracker using the New Term Request form.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sequencing",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlIssues",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100560",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The details surrounding a low quality determination in a quality control assessment.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Quality control details",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "CT value of 39. Low viral load. Low DNA concentration after amplification.",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Provide notes or details regarding QC results using free text.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "qualityControlDetails",
"required": [],
"title": "name",
"type": "string"
},
"ontology_id": {
"default": "GENEPIO:0100561",
"required": [],
"title": "ontology_id",
"type": "string"
}
},
"required": [
"name",
"ontology_id",
"definition",
"guidance",
"example",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Diagnostic measurement method",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticMeasurementMethod",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Diagnostic target presence",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticTargetPresence",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Gene name",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticTargetGeneName",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Diagnostic measurement value",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticMeasurementValue",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Diagnostic measurement unit",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Diagnostics",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "diagnosticMeasurementUnit",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Length",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Alignment states and QC metrics",
"required": [],
"title": "header",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "length",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
},
"rangeSearch": {
"default": true,
"required": [],
"title": "rangeSearch",
"type": "boolean"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"header",
"noInput",
"rangeSearch",
"initiallyVisible",
"perSegment",
"displayName"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiHostName",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "hostNameScientific",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"generateIndex",
"autocomplete",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiHostCommonName",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "hostNameCommon",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"generateIndex",
"autocomplete",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=info\u0026id=__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiHostTaxId",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "hostTaxonId",
"required": [],
"title": "name",
"type": "string"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
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"type",
"autocomplete",
"customDisplay",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiIsLabHost",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "isLabHost",
"required": [],
"title": "name",
"type": "string"
},
"type": {
"default": "boolean",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
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"type",
"autocomplete",
"header",
"ingest"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "cellLine",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
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"generateIndex",
"autocomplete",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "passageNumber",
"required": [],
"title": "name",
"type": "string"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Host",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "passageMethod",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"generateIndex",
"autocomplete",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "ncbiSourceDb",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
}
},
"required": [
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"generateIndex",
"autocomplete",
"header",
"hideOnSequenceDetailsPage",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "ncbiVirusName",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
}
},
"required": [
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"generateIndex",
"autocomplete",
"hideOnSequenceDetailsPage",
"noInput",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide\u0026VirusLineage_ss=taxid:__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
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"url"
],
"title": "customDisplay",
"type": "object"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "ncbiVirusTaxId",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
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"type",
"autocomplete",
"customDisplay",
"hideOnSequenceDetailsPage",
"noInput",
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],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
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"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/sra/?term=__value__",
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"title": "url",
"type": "string"
}
},
"required": [
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"url"
],
"title": "customDisplay",
"type": "object"
},
"displayName": {
"default": "SRA run accession",
"required": [],
"title": "displayName",
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},
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"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiSraAccessions",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "sraRunAccession",
"required": [],
"title": "name",
"type": "string"
},
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"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
}
},
"required": [
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"customDisplay",
"header",
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],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
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"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/NP.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence"
],
"type": "object"
}
],
"required": []
},
"required": [],
"title": "genes",
"type": "array"
},
"nucleotideSequences": {
"items": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"insdcAccessionFull": {
"default": "NC_005301.3",
"required": [],
"title": "insdcAccessionFull",
"type": "string"
},
"name": {
"default": "L",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/reference_L.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence",
"insdcAccessionFull"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"insdcAccessionFull": {
"default": "NC_005300.2",
"required": [],
"title": "insdcAccessionFull",
"type": "string"
},
"name": {
"default": "M",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/reference_M.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence",
"insdcAccessionFull"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"insdcAccessionFull": {
"default": "NC_005302.1",
"required": [],
"title": "insdcAccessionFull",
"type": "string"
},
"name": {
"default": "S",
"required": [],
"title": "name",
"type": "string"
},
"sequence": {
"default": "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/reference_S.fasta]]",
"required": [],
"title": "sequence",
"type": "string"
}
},
"required": [
"name",
"sequence",
"insdcAccessionFull"
],
"type": "object"
}
],
"required": []
},
"required": [],
"title": "nucleotideSequences",
"type": "array"
}
},
"required": [
"nucleotideSequences",
"genes"
],
"title": "referenceGenomes",
"type": "object"
},
"schema": {
"additionalProperties": false,
"properties": {
"\u003c\u003c": {
"additionalProperties": false,
"properties": {
"earliestReleaseDate": {
"additionalProperties": false,
"properties": {
"enabled": {
"default": true,
"required": [],
"title": "enabled",
"type": "boolean"
},
"externalFields": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "externalFields",
"type": "array"
}
},
"required": [
"enabled",
"externalFields"
],
"title": "earliestReleaseDate",
"type": "object"
},
"extraInputFields": {
"items": {
"required": []
},
"required": [],
"title": "extraInputFields",
"type": "array"
},
"image": {
"default": "/images/organisms/ebolasudan_small.jpg",
"required": [],
"title": "image",
"type": "string"
},
"loadSequencesAutomatically": {
"default": true,
"required": [],
"title": "loadSequencesAutomatically",
"type": "boolean"
},
"metadata": {
"description": "# TODO: Allow extra metadata field by particular organisms (e.g. clade/lineage)",
"items": {
"anyOf": [
{
"additionalProperties": false,
"properties": {
"columnWidth": {
"default": 100,
"required": [],
"title": "columnWidth",
"type": "integer"
},
"displayName": {
"default": "Collection date",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "ncbiCollectionDate",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "sampleCollectionDate",
"required": [],
"title": "name",
"type": "string"
},
"notSearchable": {
"default": true,
"required": [],
"title": "notSearchable",
"type": "boolean"
},
"order": {
"default": 10,
"required": [],
"title": "order",
"type": "integer"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"fieldType": {
"default": "dateRangeString",
"required": [],
"title": "fieldType",
"type": "string"
}
},
"required": [
"fieldType"
],
"title": "args",
"type": "object"
},
"function": {
"default": "parse_date_into_range",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleCollectionDate",
"required": [],
"title": "date",
"type": "string"
},
"releaseDate": {
"default": "ncbiReleaseDate",
"required": [],
"title": "releaseDate",
"type": "string"
}
},
"required": [
"date",
"releaseDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"required": {
"default": true,
"required": [],
"title": "required",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"header",
"ingest",
"order",
"preprocessing",
"required",
"notSearchable",
"columnWidth"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Collection date (lower bound)",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "sampleCollectionDateRangeLower",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"fieldType": {
"default": "dateRangeLower",
"required": [],
"title": "fieldType",
"type": "string"
}
},
"required": [
"fieldType"
],
"title": "args",
"type": "object"
},
"function": {
"default": "parse_date_into_range",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleCollectionDate",
"required": [],
"title": "date",
"type": "string"
},
"releaseDate": {
"default": "ncbiReleaseDate",
"required": [],
"title": "releaseDate",
"type": "string"
}
},
"required": [
"date",
"releaseDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"rangeOverlapSearch": {
"additionalProperties": false,
"properties": {
"bound": {
"default": "lower",
"required": [],
"title": "bound",
"type": "string"
},
"rangeDisplayName": {
"default": "Collection date",
"required": [],
"title": "rangeDisplayName",
"type": "string"
},
"rangeName": {
"default": "sampleCollectionDateRange",
"required": [],
"title": "rangeName",
"type": "string"
}
},
"required": [
"rangeName",
"rangeDisplayName",
"bound"
],
"title": "rangeOverlapSearch",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"initiallyVisible",
"header",
"preprocessing",
"rangeOverlapSearch",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Collection date (upper bound)",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "sampleCollectionDateRangeUpper",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"fieldType": {
"default": "dateRangeUpper",
"required": [],
"title": "fieldType",
"type": "string"
}
},
"required": [
"fieldType"
],
"title": "args",
"type": "object"
},
"function": {
"default": "parse_date_into_range",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"date": {
"default": "sampleCollectionDate",
"required": [],
"title": "date",
"type": "string"
},
"releaseDate": {
"default": "ncbiReleaseDate",
"required": [],
"title": "releaseDate",
"type": "string"
}
},
"required": [
"date",
"releaseDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
},
"rangeOverlapSearch": {
"additionalProperties": false,
"properties": {
"bound": {
"default": "upper",
"required": [],
"title": "bound",
"type": "string"
},
"rangeDisplayName": {
"default": "Collection date",
"required": [],
"title": "rangeDisplayName",
"type": "string"
},
"rangeName": {
"default": "sampleCollectionDateRange",
"required": [],
"title": "rangeName",
"type": "string"
}
},
"required": [
"rangeName",
"rangeDisplayName",
"bound"
],
"title": "rangeOverlapSearch",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"initiallyVisible",
"header",
"preprocessing",
"rangeOverlapSearch",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"name": {
"default": "displayName",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"args": {
"additionalProperties": false,
"properties": {
"order": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "order",
"type": "array"
},
"type": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
},
{
"required": [],
"type": "string"
}
],
"required": []
},
"required": [],
"title": "type",
"type": "array"
}
},
"required": [
"order",
"type"
],
"title": "args",
"type": "object"
},
"function": {
"default": "concatenate",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"geoLocCountry": {
"default": "geoLocCountry",
"required": [],
"title": "geoLocCountry",
"type": "string"
},
"sampleCollectionDate": {
"default": "sampleCollectionDate",
"required": [],
"title": "sampleCollectionDate",
"type": "string"
}
},
"required": [
"geoLocCountry",
"sampleCollectionDate"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs",
"args"
],
"title": "preprocessing",
"type": "object"
}
},
"required": [
"name",
"preprocessing",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"columnWidth": {
"default": 100,
"required": [],
"title": "columnWidth",
"type": "integer"
},
"displayName": {
"default": "NCBI release date",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "ncbiReleaseDate",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "parse_timestamp",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"timestamp": {
"default": "ncbiReleaseDate",
"required": [],
"title": "timestamp",
"type": "string"
}
},
"required": [
"timestamp"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"type",
"header",
"preprocessing",
"noInput",
"columnWidth"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Earliest release date",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "earliestReleaseDate",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"rangeSearch": {
"default": true,
"required": [],
"title": "rangeSearch",
"type": "boolean"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header",
"type",
"rangeSearch",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"columnWidth": {
"default": 100,
"required": [],
"title": "columnWidth",
"type": "integer"
},
"displayName": {
"default": "NCBI update date",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "ncbiUpdateDate",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
},
"preprocessing": {
"additionalProperties": false,
"properties": {
"function": {
"default": "parse_timestamp",
"required": [],
"title": "function",
"type": "string"
},
"inputs": {
"additionalProperties": false,
"properties": {
"timestamp": {
"default": "ncbiUpdateDate",
"required": [],
"title": "timestamp",
"type": "string"
}
},
"required": [
"timestamp"
],
"title": "inputs",
"type": "object"
}
},
"required": [
"function",
"inputs"
],
"title": "preprocessing",
"type": "object"
},
"type": {
"default": "date",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"displayName",
"header",
"preprocessing",
"noInput",
"perSegment",
"oneHeader",
"columnWidth"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Latitude",
"required": [],
"title": "displayName",
"type": "string"
},
"guidance": {
"default": "Geo-coordinate latitude in decimal degree (WGS84) format, i.e. values in range -90 to 90, where positive values are north of the Equator.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "geoLocLatitude",
"required": [],
"title": "name",
"type": "string"
},
"type": {
"default": "float",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header",
"type",
"guidance"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Longitude",
"required": [],
"title": "displayName",
"type": "string"
},
"guidance": {
"default": "Geo-coordinate longitude in decimal degree (WGS84) format, i.e. values in range -180 to 180, where positive values are east of the Prime Meridian.",
"required": [],
"title": "guidance",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "geoLocLongitude",
"required": [],
"title": "name",
"type": "string"
},
"type": {
"default": "float",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header",
"type",
"guidance"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"autocomplete": {
"default": true,
"required": [],
"title": "autocomplete",
"type": "boolean"
},
"displayName": {
"default": "Collection country",
"required": [],
"title": "displayName",
"type": "string"
},
"generateIndex": {
"default": true,
"required": [],
"title": "generateIndex",
"type": "boolean"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "country",
"required": [],
"title": "ingest",
"type": "string"
},
"initiallyVisible": {
"default": true,
"required": [],
"title": "initiallyVisible",
"type": "boolean"
},
"name": {
"default": "geoLocCountry",
"required": [],
"title": "name",
"type": "string"
},
"order": {
"default": 20,
"required": [],
"title": "order",
"type": "integer"
},
"preprocessing": {
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"properties": {
"args": {
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"properties": {
"options": {
"items": {
"anyOf": [
{
"required": [],
"type": "string"
},
{
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"type": "string"
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{
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},
{
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},
{
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},
{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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{
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"type": "boolean"
}
},
"required": [
"name",
"displayName",
"generateIndex",
"autocomplete",
"hideOnSequenceDetailsPage",
"noInput",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "insdcAccessionBase",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
}
},
"required": [
"name",
"header",
"hideOnSequenceDetailsPage",
"noInput",
"perSegment",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"hideOnSequenceDetailsPage": {
"default": true,
"required": [],
"title": "hideOnSequenceDetailsPage",
"type": "boolean"
},
"name": {
"default": "insdcVersion",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
},
"type": {
"default": "int",
"required": [],
"title": "type",
"type": "string"
}
},
"required": [
"name",
"type",
"header",
"hideOnSequenceDetailsPage",
"noInput",
"perSegment",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/nuccore/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"displayName": {
"default": "INSDC accession",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "genbankAccession",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "insdcAccessionFull",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
},
"perSegment": {
"default": true,
"required": [],
"title": "perSegment",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"customDisplay",
"header",
"ingest",
"noInput",
"perSegment",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/bioproject/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"ingest": {
"default": "bioprojects",
"required": [],
"title": "ingest",
"type": "string"
},
"name": {
"default": "bioprojectAccession",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
}
},
"required": [
"name",
"customDisplay",
"header",
"ingest",
"noInput"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/datasets/genome/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"displayName": {
"default": "GCA accession",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "gcaAccession",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
}
},
"required": [
"name",
"displayName",
"customDisplay",
"header",
"noInput",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"customDisplay": {
"additionalProperties": false,
"properties": {
"type": {
"default": "link",
"required": [],
"title": "type",
"type": "string"
},
"url": {
"default": "https://www.ncbi.nlm.nih.gov/biosample/__value__",
"required": [],
"title": "url",
"type": "string"
}
},
"required": [
"type",
"url"
],
"title": "customDisplay",
"type": "object"
},
"header": {
"default": "INSDC",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "biosampleAccession",
"required": [],
"title": "name",
"type": "string"
},
"noInput": {
"default": true,
"required": [],
"title": "noInput",
"type": "boolean"
},
"oneHeader": {
"default": true,
"required": [],
"title": "oneHeader",
"type": "boolean"
}
},
"required": [
"name",
"customDisplay",
"header",
"noInput",
"oneHeader"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"displayName": {
"default": "Culture ID",
"required": [],
"title": "displayName",
"type": "string"
},
"header": {
"default": "Sample details",
"required": [],
"title": "header",
"type": "string"
},
"name": {
"default": "cultureId",
"required": [],
"title": "name",
"type": "string"
}
},
"required": [
"name",
"displayName",
"header"
],
"type": "object"
},
{
"additionalProperties": false,
"properties": {
"definition": {
"default": "The date on which the sample was received by the laboratory.",
"required": [],
"title": "definition",
"type": "string"
},
"displayName": {
"default": "Sample received date",
"required": [],
"title": "displayName",
"type": "string"
},
"example": {
"default": "2020-03-20",
"required": [],
"title": "example",
"type": "string"
},
"guidance": {
"default": "Alternative if \"sampleCollectionDate\" is not available. Record the date the sample was received by the laboratory. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add \"jitter\" to the received date by adding or subtracting calendar days. Do not change the received date in your original records. Alternatively, collection_date may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format \"YYYY-MM-DD\".",
"required
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