{
  "$id": "http://example.com/example.json",
  "type": "object",
  "properties": {
    "uniprot_canonical_id": {
      "$id": "/properties/uniprot_canonical_id",
      "type": "string",
      "description": "ID of the protein using Uniprot entry name.",
      "examples": ["SHBG_HUMAN"]
    },
    "uniprot_canonical_ac": {
      "$id": "/properties/uniprot_canonical_ac",
      "type": "string",
      "description": "Accession ID of the protein using Uniprot entry ID",
      "examples": ["P04278"]
    },
    "mass": {
      "$id": "/properties/mass",
      "type": "object",
      "description": "Mass of the protein.",
      "properties": {
        "chemical_mass": {
          "$id": "/properties/recommendedName/properties/chemical_mass",
          "type": "number",
          "description": "Chemical mass.",
          "examples": [50638]
        }
      }
    },
    "recommendedName": {
      "$id": "/properties/recommendedName",
      "type": "object",
      "description": "Object with a tuple of short and long name for the protein. It is possible that one of the names is missing.",
      "properties": {
        "full": {
          "$id": "/properties/recommendedName/properties/full",
          "type": "string",
          "description": "Full name of the protein.",
          "examples": ["Sex hormone-binding globulin"]
        },
        "short": {
          "$id": "/properties/recommendedName/properties/short",
          "type": "string",
          "description": "Corresponding short name of the protein.",
          "examples": ["SHBG"]
        }
      }
    },

    "sequence": {
      "$id": "/properties/sequence",
      "type": "object",
      "description": "Sequence object for the protein. It contains the amino acid sequence and the sequence length (number of amino acids.",
      "properties": {
        "sequence": {
          "$id": "/properties/sequence/properties/sequence",
          "type": "string",
          "description": "Amino acid sequence of the protein.",
          "default": "",
          "examples": [
            "MESRGPLATSRLLLLLLLLLLRHTRQGWALRPVLPTQSAHDPPAVHLSNGPGQEPIAVMTFDLTKITKTSSSFEVRTWDPEGVIFYGDTNPKDDWFMLGLRDGRPEIQ"
          ]
        },
        "length": {
          "$id": "/properties/sequence/properties/length",
          "type": "integer",
          "description": "Number of amino acides in the sequence.",
          "examples": [402]
        }
      },
      "required": ["sequence"]
    },
    "keywords": {
      "$id": "/properties/keywords",
      "type": "array",
      "description": "List of keywords that annotate the protein. The keyword concept is identical to the one in UniProt.",
      "items": {
        "$id": "/properties/keywords/items",
        "type": "string",
        "description": "String representing the keyword.",
        "examples": ["3D-structure"]
      }
    },

    "glycosylation": {
      "$id": "/properties/glycosylation",
      "type": "array",
      "description": "List of glycosylations.",
      "items": {
        "$id": "/properties/glycosylation/items",
        "type": "object",
        "description": "Glycosylation object that contains the glycosylated amino acid, the positon of this amino acid, the reported glycan and a list of evidence for this annotation.",
        "properties": {
          "residue": {
            "$id": "/properties/glycosylation/items/properties/residue",
            "type": "string",
            "description": "Amino acid residue that is glycosylated (one letter code).",
            "examples": ["T"]
          },
          "position": {
            "$id": "/properties/glycosylation/items/properties/position",
            "type": "integer",
            "description": "Position of the amino acid residue in the protein sequence.",
            "examples": [36]
          },
          "glytoucan_ac": {
            "$id": "/properties/glycosylation/items/properties/glytoucan_ac",
            "type": "string",
            "description": "ID of the glycan represented as GlyTouCan ID.",
            "examples": ["G123456"]
          },
          "type": {
            "$id": "/properties/glycosylation/items/properties/type",
            "type": "string",
            "description": "Type of glycosylation (e.g. N-Glycan).",
            "examples": ["N-Glycan"]
          },
          "evidence": {
            "$id": "/properties/glycosylation/items/properties/evidence",
            "type": "array",
            "description": "List of evidence objects.",
            "items": {
              "$id": "/properties/glycosylation/items/properties/evidence/items",
              "type": "object",
              "description": "Evidence object that stores the database name, entry ID and URL. The objects refers to an entry on another database that provided this glycosylation annotation.",
              "properties": {
                "database": {
                  "$id": "/properties/glycosylation/items/properties/evidence/items/properties/database",
                  "type": "string",
                  "description": "Name of the database that provided this glycosylation annotation.",
                  "default": "",
                  "examples": ["UniProt"]
                },
                "id": {
                  "$id": "/properties/glycosylation/items/properties/evidence/items/properties/id",
                  "type": "string",
                  "description": "Databases entry that provides this glycosylation annotation.",
                  "default": "",
                  "examples": ["P04278"]
                },
                "url": {
                  "$id": "/properties/glycosylation/items/properties/evidence/items/properties/url",
                  "type": "string",
                  "description": "Link to the database entry that provided this glycosylation annotation.",
                  "default": "",
                  "examples": ["http://glycomics.ccrc.uga.edu/ontologies"]
                }
              },
              "required": ["database"]
            }
          }
        },
        "required": ["type", "evidence"]
      }
    },

    "mutation": {
      "$id": "/properties/mutation",
      "type": "array",
      "description": "List of mutations in the gene.",
      "items": {
        "$id": "/properties/mutation/items",
        "type": "object",
        "description": "Object describing a mutation.",
        "properties": {
          "annotation": {
            "$id": "/properties/mutation/items/properties/annotation",
            "type": "string",
            "description": "Description of the mutation.",
            "default": "",
            "examples": [
              "High frequency non-synonymous mutation in BRCA (DOID:001) cancer"
            ]
          }
        }
      }
    }
  },
  "site_annotation": {
    "$id": "/properties/site_annotation",
    "type": "array",
    "description": "List of site_annotation in the protein.",
    "items": {
      "$id": "/properties/site_annotation/items",
      "type": "object",
      "description": "Object describing a site_annotation.",
      "properties": {
        "start_pos": {
          "$id": "/properties/isoforms/items/properties/site_annotation/properties/start_pos",
          "type": "integer",
          "description": "Start position (number of base) where the site_annotation begins.",
          "examples": [1233131]
        },
        "end_pos": {
          "$id": "/properties/isoforms/items/properties/site_annotation/properties/end_pos",
          "type": "integer",
          "description": "End position (number of base) the site_annotation ends with.",
          "examples": [332423]
        },
        "annotation": {
          "$id": "/properties/site_annotation/items/properties/annotation",
          "type": "string",
          "description": "Description of the site_annotation.",
          "default": "",
          "examples": [
            "High frequency non-synonymous site_annotation in BRCA (DOID:001) cancer"
          ]
        }
      }
    }
  }
}