plant-miappe-validation.json

{
  "id": "https://www.ebi.ac.uk/biosamples/schemas/plant-miappe.json",
  "$schema": "http://json-schema.org/draft-07/schema#",
  "title": "ENA Plant MIAPPE Checklist for omics and phenomic interoperability",
  "version": "1.2",
  "description": "ENA Plant MIAPPE Checklist for omics and phenomic interoperability",
  "type": "object",
  "$async": true,
  "definitions": {
    "attribute_value": {
      "type": "object",
      "additionalProperties": false,
      "properties": {
        "text": {
          "type": "string"
        },
        "ontologyTerms": {
          "type": "array",
          "items": {
            "type": "string",
            "format": "uri",
            "isValidTerm": true
          }
        },
        "unit": {
          "description": "The unit associated with the attribute value",
          "type": "string"
        }
      }
    },
    "attribute_value_list": {
      "type": "array",
      "items": {
        "$ref": "#/definitions/attribute_value"
      }
    },
    "geo_location": {
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "text": {
            "type": "string",
            "pattern": "(^.*[+-]?[0-9]+.?[0-9]*.*$)|(^not collected$)|(^not provided$)|(^restricted access$)"
          }
        }
      }
    }
  },
  "properties": {
    "characteristics": {
      "description": "All the characteristics associated to the sample",
      "type": "object",
      "properties": {
        "project name": {
          "description": "Project name.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "biological material ID": {
          "description": "(DM-41) Biological material ID.",
          "cardinality": "mandatory",
          "$ref": "#/definitions/attribute_value_list"
        },
        "organism": {
          "description": "(DM-42) Organism.",
          "cardinality": "mandatory",
          "$ref": "#/definitions/attribute_value_list"
        },
        "genus": {
          "description": "(DM-43) Genus.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "species": {
          "description": "(DM-44) Species.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "infraspecific name": {
          "description": "(DM-44) Infraspecific name.",
          "cardinality": "recommended",
          "$ref": "#/definitions/attribute_value_list"
        },
        "ecotype": {
          "description": "Ecotype.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "biological material latitude": {
          "description": "(DM-45) Biological material latitude.",
          "cardinality": "optional",
          "allOf": [
            {
              "$ref": "#/definitions/attribute_value_list"
            },
            {
              "$ref": "#/definitions/geo_location"
            }
          ]
        },
        "biological material longitude": {
          "description": "(DM-46) Biological material longitude.",
          "cardinality": "optional",
          "allOf": [
            {
              "$ref": "#/definitions/attribute_value_list"
            },
            {
              "$ref": "#/definitions/geo_location"
            }
          ]
        },
        "biological material altitude": {
          "description": "(DM-47) Biological material altitude.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "biological material coordinates uncertainty": {
          "description": "(DM-48) Biological material coordinates uncertainty.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "biological material geographic location": {
          "description": "Biological material geographic location (country and/or sea).",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "biological material preprocessing": {
          "description": "(DM-49) Biological material preprocessing.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "material source ID": {
          "description": "(DM-50) Material source ID (Holding institute/stock centre, accession).",
          "cardinality": "recommended",
          "$ref": "#/definitions/attribute_value_list"
        },
        "material source DOI": {
          "description": "(DM-51) Material source DOI.",
          "cardinality": "recommended",
          "$ref": "#/definitions/attribute_value_list",
          "allOf": [
            {
              "$ref": "#/definitions/attribute_value_list"
            },
            {
              "type": "array",
              "items":{
                "type": "string",
                "pattern": "^doi:.*$"
              },
              "maxItem":1
            }
          ]
        },
        "material source latitude": {
          "description": "(DM-52) Material source latitude.",
          "cardinality": "optional",
          "allOf": [
            {
              "$ref": "#/definitions/attribute_value_list"
            },
            {
              "$ref": "#/definitions/geo_location"
            }
          ]
        },
        "material source longitude": {
          "description": "(DM-53) Material source longitude.",
          "cardinality": "optional",
          "allOf": [
            {
              "$ref": "#/definitions/attribute_value_list"
            },
            {
              "$ref": "#/definitions/geo_location"
            }
          ]
        },
        "material source altitude": {
          "description": "(DM-54) Material source altitude.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "material source coordinates uncertainty": {
          "description": "(DM-55) Material source coordinates uncertainty.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "material source description": {
          "description": "(DM-56) Material source description.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "material source geographic location": {
          "description": "Material source geographic location (country and/or sea).",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "biological material ploidy": {
          "description": "Biological material ploidy.",
          "cardinality": "recommended",
          "$ref": "#/definitions/attribute_value_list"
        },
        "collected by": {
          "description": "Collected by.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "collection date": {
          "description": "Collection date.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "sex": {
          "description": "Sex.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "environment (biome)": {
          "description": "Environment (biome).",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "plant structure development stage": {
          "description": "DM-77 Plant structure development stage.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "plant anatomical entity": {
          "description": "DM-78 Plant anatomical entity.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "sample description": {
          "description": "DM-79 Sample description.",
          "cardinality": "recommended",
          "$ref": "#/definitions/attribute_value_list"
        },
        "sample ID": {
          "description": "DM-75 Sample ID.",
          "cardinality": "recommended",
          "$ref": "#/definitions/attribute_value_list"
        },
        "environment parameter": {
          "description": "DM-58 Environment parameter.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        },
        "environment parameter value": {
          "description": "DM-59 Environment parameter value.",
          "cardinality": "optional",
          "$ref": "#/definitions/attribute_value_list"
        }
      },
      "required": [
        "biological material ID",
        "organism"
      ],
      "dependencies": {
        "environment parameter":["environment parameter value"],
        "environment parameter value":["environment parameter"]
      },
      "additionalProperties": true
    }
  }
}