{
  "$schema": "http://json-schema.org/draft-07/schema#",
  "$id": "https://schema.humancellatlas.org/type/biomaterial/11.0.0/specimen_from_organism",
  "description": "Information about the specimen that was collected from the donor organism.",
  "additionalProperties": false,
  "required": [
    "describedBy",
    "schema_type",
    "biomaterial_core",
    "organ"
  ],
  "title": "Specimen from organism",
  "name": "specimen_from_organism",
  "type": "object",
  "properties": {
    "describedBy": {
      "description": "The URL reference to the schema.",
      "type": "string",
      "pattern": "^(http|https)://schema.(.*?)humancellatlas.org/type/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/specimen_from_organism"
    },
    "schema_version": {
      "description": "The version number of the schema in major.minor.patch format.",
      "type": "string",
      "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
      "example": "4.6.1"
    },
    "schema_type": {
      "description": "The type of the metadata schema entity.",
      "type": "string",
      "enum": [
        "biomaterial"
      ]
    },
    "provenance": {
      "description": "Provenance information provided by the system.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/system/1.1.0/provenance"
    },
    "biomaterial_core": {
      "description": "Core biomaterial-level information.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/core/biomaterial/8.4.0/biomaterial_core",
      "user_friendly": "Biomaterial core"
    },
    "genus_species": {
      "description": "The scientific binomial name for the species of the specimen.",
      "type": "array",
      "items": {
        "$ref": "https://schema.humancellatlas.org/module/ontology/5.3.5/species_ontology"
      },
      "user_friendly": "Genus species"
    },
    "organ": {
      "description": "The organ that the biomaterial came from.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/ontology/5.3.7/organ_ontology",
      "guidelines": "Blood and connective tissue are considered organs.",
      "user_friendly": "Organ"
    },
    "organ_parts": {
      "description": "A term for a specific part of the organ that the biomaterial came from.",
      "type": "array",
      "items": {
        "$ref": "https://schema.humancellatlas.org/module/ontology/5.3.5/organ_part_ontology"
      },
      "guidelines": "The term organ part is very broadly defined here.",
      "user_friendly": "Organ part"
    },
    "transplant_organ": {
      "description": "Was the specimen collected after extraction for organ transplantation?",
      "type": "boolean",
      "user_friendly": "Transplant organ",
      "guidelines": "Should be one of: yes, or no.",
      "example": "yes; no"
    },
    "diseases": {
      "description": "Short description of known disease(s) of the specimen.",
      "type": "array",
      "items": {
        "$ref": "https://schema.humancellatlas.org/module/ontology/5.4.0/disease_ontology"
      },
      "user_friendly": "Known disease(s)",
      "guidelines": "Enter normal if no known diseases."
    },
    "adjacent_diseases": {
      "description": "Short description of the disease(s) adjacent to the specimen's collection site (e.g. breast cancer).",
      "type": "array",
      "items": {
        "$ref": "https://schema.humancellatlas.org/module/ontology/5.4.0/disease_ontology"
      },
      "user_friendly": "Adjacent disease(s)",
      "guidelines": "If a healthy specimen is sampled from a site adjacent to diseased tissue, enter that tissue's disease here. If no diseased tissue is adjacent to the specimen, leave blank."
    },
    "state_of_specimen": {
      "description": "State of the specimen at the time of collection.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/biomaterial/6.0.0/state_of_specimen",
      "user_friendly": "State of specimen"
    },
    "preservation_storage": {
      "description": "Information about how a specimen was preserved and/or stored over a period of time.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/biomaterial/6.1.1/preservation_storage",
      "user_friendly": "Preservation/Storage"
    },
    "collection_time": {
      "description": "When the biomaterial was collected.",
      "type": "string",
      "user_friendly": "Time of collection",
      "example": "2016-01-21T00:00:00Z; 2016-03",
      "guidelines": "Enter the time in date-time format: yyyy-mm-ddThh:mm:ssZ. Supplying partial date is allowed.",
      "oneOf": [
        {
          "format": "date-time"
        },
        {
          "pattern": "^((19|20)\\d\\d){1}([- \\./][01]\\d){0,1}([- \\./][0-3]\\d){0,1}$"
        }
      ]
    },
    "collection_institute": {
      "description": "Institute where the biomaterial was collected on.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/biomaterial/1.0.0/collection_institute",
      "user_friendly": "Collection institute"
    },
    "purchased_specimen": {
      "description": "Information about a purchased specimen.",
      "type": "object",
      "$ref": "https://schema.humancellatlas.org/module/process/6.1.0/purchased_reagents",
      "user_friendly": "Purchased specimen"
    }
  }
}