National Center for Biotechnology Information (NCBI) · Schema

v2VirusDatasetRequest

Schema for v2VirusDatasetRequest

BioinformaticsGenomicsLife SciencesPubMedSequencesBLASTTaxonomyChemistryOpen Access

Properties

Name	Type	Description
accessions	array
taxon	string
taxons	array
refseq_only	boolean
annotated_only	boolean
released_since	string
updated_since	string
host	string
pangolin_classification	string
geo_location	string
usa_state	string
complete_only	boolean
table_fields	array
include_sequence	array
aux_report	array
format	object
use_psg	boolean

View JSON Schema on GitHub

JSON Schema

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://kinlane.github.io/ncbi/json-schema/v2VirusDatasetRequest.json",
  "title": "v2VirusDatasetRequest",
  "description": "Schema for v2VirusDatasetRequest",
  "type": "object",
  "properties": {
    "accessions": {
      "type": "array",
      "items": {
        "type": "string"
      }
    },
    "taxon": {
      "type": "string",
      "title": "NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank"
    },
    "taxons": {
      "type": "array",
      "items": {
        "type": "string"
      }
    },
    "refseq_only": {
      "type": "boolean",
      "title": "If true, limit results to RefSeq genomes."
    },
    "annotated_only": {
      "type": "boolean",
      "title": "If true, limit results to annotated genomes."
    },
    "released_since": {
      "type": "string",
      "format": "date-time"
    },
    "updated_since": {
      "type": "string",
      "format": "date-time"
    },
    "host": {
      "type": "string",
      "title": "Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name)."
    },
    "pangolin_classification": {
      "type": "string",
      "title": "Limit to SARS-CoV-2 genomes from the specified Pango lineage."
    },
    "geo_location": {
      "type": "string",
      "title": "Limit to genomes collected from the specified geographic location."
    },
    "usa_state": {
      "type": "string",
      "title": "Limit to genomes collected from the specified U.S. state (two-letter abbreviation)."
    },
    "complete_only": {
      "type": "boolean",
      "title": "Limit to genomes designated as complete, as defined by the submitter."
    },
    "table_fields": {
      "type": "array",
      "items": {
        "$ref": "#/components/schemas/v2VirusTableField"
      }
    },
    "include_sequence": {
      "type": "array",
      "items": {
        "$ref": "#/components/schemas/v2ViralSequenceType"
      }
    },
    "aux_report": {
      "type": "array",
      "items": {
        "$ref": "#/components/schemas/v2VirusDatasetReportType"
      }
    },
    "format": {
      "$ref": "#/components/schemas/v2TableFormat",
      "title": "Choose download format (tsv, csv or jsonl)"
    },
    "use_psg": {
      "type": "boolean",
      "title": "Experimental approach to retrieving sequence data."
    }
  }
}