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@luissian
luissian committed Jan 26, 2022
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166 changes: 166 additions & 0 deletions schema/gisaid_V0.json
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{
"$schema": "http://json-schema.org/draft/2022-01/gisaid_schema#",
"required": [
"type",
"virus_name",
"submitter",
"originating_lab",
"address",
"collection_date",
"location",
"host",
"patient_age",
"gender",
"sequencing_technology",
"fasta_filename",
],
"type": "object",
"properties": {
"type": {
"examples": ["betacoronavirus"],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "default must remain betacoronavirus",
"clasification":"Database Identifiers",
},
"virus_name": {
"examples": ["e.g. hCoV-19/Netherlands/Gelderland-01/2020 (Must be FASTA-Header from the FASTA file all_sequences.fasta)"],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "The user-defined GISAID virus name assigned to the sequence.",
"clasification":"Database Identifiers",
},
"submitter": {
"examples": ["Public Health Agency of Canada"],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "enter your GISAID-Username",
"clasification":"Database Identifiers",
},
"originating_lab": {
"examples": [""],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "Where the clinical specimen or virus isolate was first obtained",
"clasification":"Sample collection and processing",
},
"address": {
"examples": [""],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "The mailing address of the agency submitting the sample.",
"clasification":"Sample collection and processing",
},
"collection_date": {
"examples": [""],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "Date in the format YYYY or YYYY-MM or YYYY-MM-DD. Caution: collection date may be considered public health identifiable information. If this date is considered identifiable, it is acceptable to add 'jitter' to the collection date by adding or subtracting a calendar day (acceptable by GISAID). Do not change the collection date in your original records. Alternatively, ”received 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.",
"format":"date",
"clasification":"Sample collection and processing",
},
"location": {
"examples": ["e.g. Europe / Germany / Bavaria / Munich"],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "The country of origin of the sample.",
"clasification":"Sample collection and processing",
},
"host": {
"examples": ["e.g. Human, Environment, Canine, Manis javanica, Rhinolophus affinis, etc"],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "The taxonomic, or scientific name of the host.",
"clasification":"Host information",
},
"patient_age": {
"Enums": [
"0 - 9 [GENEPIO:0100049]",
"10 - 19 [GENEPIO:0100050]",
"20 - 29 [GENEPIO:0100051]",
"30 - 39 [GENEPIO:0100052]",
"40 - 49 [GENEPIO:0100053]",
"50 - 59 [GENEPIO:0100054]",
"60 - 69 [GENEPIO:0100055]",
"70 - 79 [GENEPIO:0100056]",
"80 - 89 [GENEPIO:0100057]",
"90 - 99 [GENEPIO:0100058]",
"100+ [GENEPIO:0100059]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"examples": ["50 - 59 [GENEPIO:0100054]"],
"ontology": "GENEPIO:0001394",
"type": "string",
"description": "The age category of the host at the time of sampling.",
"clasification":"Host information",
},
"gender": {
"Enums": [
"Female [NCIT:C46110]",
"Male [NCIT:C46109]",
"Non-binary Gender [GSSO:000132]",
"Transgender (assigned male at birth) [GSSO:004004]",
"Transgender (assigned female at birth) [GSSO:004005]",
"Undeclared [NCIT:C110959]",
"Not Applicable [GENEPIO:0001619]",
"Not Collected [GENEPIO:0001620]",
"Not Provided [GENEPIO:0001668]",
"Missing [GENEPIO:0001618]",
"Restricted Access [GENEPIO:0001810]"
],
"examples": ["Male [NCIT:C46109]"],
"ontology": "GENEPIO:0001395",
"type": "string",
"description": "The gender of the host at the time of sample collection.",
"clasification":"Host information",
},
"sequencing_technology": {
"examples": ["e.g. Illumina Miseq, Sanger, Nanopore MinION, Ion Torrent, etc."],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "The model of the sequencing instrument used.",
"clasification":"Sequencing",
},
"fasta_filename": {
"examples": ["e.g. all_sequences.fasta not c:\users\meier\docs\all_sequences.fasta"],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "Filename that contains the sequence without path",
"clasification":"Bioinformatics and QC metrics",
},
"additional_host_information": {
"examples": ["e.g. Patient infected while traveling in …."],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "If the information is unknown or can not be shared, leave blank.",
"clasification":"Host information",
},
"Last vaccinated": {
"examples": ["e.g. 04/09/2021"],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "The date the host received their last dose of vaccine.",
"format":"date",
"clasification":"Host information",
},
"outbreak": {
"examples": ["Date, Location e.g. type of gathering, Family cluster, etc."],
"ontology": "GENEPIO:0001156",
"type": "string",
"description": "If the information is unknown or can not be shared, leave blank.",
"clasification":"Host information",
},
"Sampling Strategy": {
"examples": ["e.g. Sentinel surveillance (ILI), Sentinel surveillance (ARI), Sentinel surveillance (SARI), Non-sentinel-surveillance (hospital), Non-sentinel-surveillance (GP network), Longitudinal sampling on same patient(s), S gene dropout"],
"ontology": "GENEPIO:",
"type": "string",
"description": "The reason that the sample was sequenced.",
"clasification":"Sequencing",
},
}

}
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