biomaterial_core.json

{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "description": "Information about any biological material that was generated/used in the project including everything from a whole organism to subcellular components.",
  "additionalProperties": false,
  "required": [ "biomaterial_id", "ncbi_taxon_id" ],
  "title": "Biomaterial core",
  "x-name": "biomaterial_core",
  "type": "object",
  "properties": {
    "describedBy": {
      "description": "The URL reference to the schema.",
      "type": "string",
      "pattern": "^(http|https)://schema.(.*?)humancellatlas.org/core/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/biomaterial_core"
    },
    "schema_version": {
      "description": "The version number of the schema in major.minor.patch format.",
      "type": "string",
      "pattern": "^\\d+\\.\\d+\\.\\d+$",
      "x-example": "4.6.1"
    },
    "biomaterial_id": {
      "description": "A unique ID for the biomaterial.",
      "type": "string",
      "x-user_friendly": "Biomaterial ID"
    },
    "biomaterial_name": {
      "description": "A short, descriptive name for the biomaterial that need not be unique.",
      "type": "string",
      "x-user_friendly": "Biomaterial name"
    },
    "biomaterial_description": {
      "description": "A general description of the biomaterial.",
      "type": "string",
      "x-user_friendly": "Biomaterial description"
    },
    "ncbi_taxon_id": {
      "description": "A taxonomy ID (taxonID) from NCBI.",
      "type": "array",
      "items": {
        "type": "integer"
      },
      "x-user_friendly": "NCBI taxon ID",
      "x-example": 9606
    },
    "genotype": {
      "description": "Genotype of the biomaterial.",
      "type": "string",
      "x-user_friendly": "Genotype",
      "x-example": "DRB1 0401 protective allele; HLA-B*3901 allele"
    },
    "supplementary_files": {
      "description": "A list of filenames of biomaterial-level supplementary files.",
      "type": "array",
      "items": {
        "type": "string"
      },
      "x-user_friendly": "Supplementary files",
      "x-example": "sample_site_image.jpg"
    },
    "biosamples_accession": {
      "description": "A BioSamples accession.",
      "type": "string",
      "pattern": "^SAM(D|N|E([AG]?))[0-9]+$",
      "x-user_friendly": "BioSamples accession",
      "x-example": "SAMN00000000",
      "x-guidelines": "Enter accession if sample has been archived. Accession can be from the DDBJ, NCBI, or EMBL-EBI and must start with SAMD, SAMN, or SAME, respectively."
    },
    "insdc_sample_accession": {
      "description": "An International Nucleotide Sequence Database Collaboration (INSDC) sample accession.",
      "type": "string",
      "pattern": "^[DES]RS[0-9]+$",
      "x-user_friendly": "INSDC sample accession",
      "x-example": "SRS0000000",
      "x-guidelines": "Enter accession if sample has been archived. Accession can be from the DDBJ, NCBI, or EMBL-EBI and must start with DRS, SRS, or ERS, respecitvely."
    },
    "HDBR_accession": {
      "description": "A Human Developmental Biology Resource (HDBR) sample accession.",
      "type": "string",
      "pattern": "(^[0-9]{5})(,\\s[0-9]{1,},\\s[a-zA-Z]+$){0,1}",
      "x-user_friendly": "HDBR accession",
      "x-example": "34526; 14758, 2, liver",
      "x-guidelines": "Enter accession if sample has been obtained from the Human Developmental Biology Resource (HDBR)."
    },
    "timecourse": {
      "$ref": "module/biomaterial/timecourse.json"
    }
  }
}