molecular_entity_schema.json

{
  "id": "https://w3id.org/dats/schema/molecular_entity_schema.json",
  "$schema": "http://json-schema.org/draft-04/schema",
  "title": "DATS molecular entity schema",
  "description": "A physical entity of molecular scales such as proteins, nucleic acids, chemical materials. They can be abiotic, biological or synthetic origin.",
  "type": "object",
  "properties": {
    "@context": {
      "description": "The JSON-LD context",
      "anyOf": [
        {
          "type": "string"
        },
        {
          "type": "object"
        },
        {
          "type": "array"
        }
      ]
    },
    "@id": {
      "description": "The JSON-LD identifier",
      "type": "string", "format": "uri"
    },
    "@type": {
      "description": "The JSON-LD type",
      "type": "string", "enum": [ "MolecularEntity" ]},
    "identifier": {
      "description": "The identifier of the molecular entity.",
      "$ref": "identifier_info_schema.json#"
    },
    "alternateIdentifiers": {
      "description": "Alternate identifiers for the molecular entity.",
      "type": "array",
      "items": {
        "$ref": "alternate_identifier_info_schema.json#"
      }
    },
    "relatedIdentifiers": {
      "description": "Related identifiers for the molecular entity.",
      "type": "array",
      "items": {
        "$ref": "related_identifier_info_schema.json#"
      }
    },
    "name": {
      "description": "The name of the molecular entity.",
      "type" :  "string"
    },
    "description": {
      "description": "A textual narrative comprised of one or more statements describing the molecular entity.",
      "type": "string"
    },
    "taxonomy" : {
      "description": "The taxonomic information for this material (ideally specified from a controlled vocabulary/ontology).",
      "type": "array",
      "items": {
        "$ref": "taxonomic_info_schema.json#"
      }
    },
    "characteristics" : {
      "description": "The characteristic information or attributes denoting the material.",
      "type" : "array",
      "items" : {
        "oneOf": [
          {"$ref": "dimension_schema.json#"},
          {"$ref": "material_schema.json#"}
        ]
      }
    },
    "genomeLocations" : {
      "description": "The set of location information of a genetic element in a genome.",
      "type" : "array",
      "items" : {
        "$ref": "genome_location_schema.json#"
      }
    },
    "structure": {
      "description": "The primary sequence of the molecular entity (e.g. inchi code;DNA sequence in FASTA format)",
      "type" :  "string"
    },
    "roles" : {
      "description": "The roles played by the molecular entity.",
      "type" : "array",
      "items" : {
        "$ref": "annotation_schema.json#"
      }
    },
    "involvedInProcess" : {
      "description": "The molecular processes where the molecular entity is known to be involved in.",
      "type": "array",
      "items":{
        "$ref" : "activity_schema.json#"
      }
    },
    "relatedEntities": {
      "description": "Entities that are related to this molecular entity.",
      "type": "array",
      "items": {
        "type": "object",
        "properties": {
          "object": {
            "description": "The object of the relationship, i.e. the representation or identifier of the related enttity",
            "anyOf": [
              {
                "type": "object"
              },
              {
                "type": "string"
              }
            ]
          },
          "relation": {
            "description": "The type of the relationship corresponding to this molecular entity.",
            "$ref": "annotation_schema.json#"
          },
          "resultingFrom": {
            "description": "The activity (or process) that gave origin at the relationship between this molecular entity and the external entity.",
            "$ref": "activity_schema.json#"
          },
          "relationEvidence": {
            "type": "array",
            "items": {
              "type": "object",
              "properties": {
                "evidenceCodes": {
                  "description": "An array of labels and ideally an ontology term IRI (e.g. for the Evidence & Conclusion Ontology - ECO) indicating the evidence for the relationship between the molecular entity and the external entity",
                  "type": "array",
                  "items": {
                    "$ref": "annotation_schema.json#"
                  }
                },
                "publications": {
                  "description": "The list of publications providing evidence of the relationship.",
                  "type": "array",
                  "items": {
                    "$ref": "publication_schema.json#"
                  }
                },
                "dateEstablished": {
                  "description": "The date in which the evidence of the relationship was established.",
                  "$ref": "date_info_schema.json#"
                }
              }
            }
          }
        }
      }
    },
    "dates" : {
      "description": "Relevant dates for the molecular entity, a date must be added, e.g. creation date, annotation date or last modification date should be added. a type should always be provided",
      "type" : "array",
      "items" : {
        "$ref" : "date_info_schema.json#"
      }
    },
    "extraProperties": {
      "description": "Extra properties that do not fit in the previous specified attributes. ",
      "type": "array",
      "items": {
        "$ref" : "category_values_pair_schema.json#"
      }
    }
  },
  "additionalProperties": false,
  "required": [ "name" ]
}