Biolink Beacon

A knowledge beacon implementation for the Monarch Biolink API (https://api.monarchinitiative.org/api/), a biomedical data source containing information about diseases, phenotypes, and genes, and the relations between them.

Running with Docker

docker build -t biolinkbeacon .
docker run -p 8080:8080 biolinkbeacon

Navigate to http://localhost:8080/ui/ in your browser to see the Swagger UI

Usage

http://localhost:8080/concepts?keywords=FANC&pageSize=1

[
  {
    "definition": "A Fanconi anemia that has_material_basis_in homozygous or compound heterozygous mutation in the FANCA gene on chromosome 16q24.",
    "id": "MONDO:0009215",
    "name": "Fanconi anemia complementation group a",
    "synonyms": [
      "Estren-Dameshek Variant of Fanconi Anemia",
      "FANCONI ANEMIA, COMPLEMENTATION GROUP A",
      "Fanconi Anemia",
      "FANCA",
      "Fanconi Anemia, Estren-Dameshek Variant",
      "Estren-Dameshek Variant of Fanconi Pancytopenia",
      "Fanconi anemia complementation group type A",
      "FANCONI ANEMIA, COMPLEMENTATION GROUP A; FANCA",
      "Fanconi Anemia, Complementation Group type a"
    ],
    "type": "disease"
  }
]

http://localhost:8080/statements?s=MONDO:0009215&pageSize=1

[
  {
    "id": "biolink:06c7f4a5-65e5-4243-bbdd-ab92ced62997",
    "object": {
      "id": "HP:0000252",
      "name": "Microcephaly",
      "type": "phenotype"
    },
    "predicate": {
      "id": "RO:0002200",
      "name": "has phenotype"
    },
    "subject": {
      "id": "MONDO:0009215",
      "name": "Fanconi anemia complementation group a",
      "type": "disease"
    }
  }
]

http://localhost:8080/concepts/HP:0000252

[
  {
    "id": "HP:0000252",
    "name": "Microcephaly",
    "synonyms": [
      "Reduced head circumference",
      "Abnormally small skull",
      "Decreased size of cranium",
      "Decreased circumference of cranium",
      "small cranium",
      "Small head circumference",
      "Abnormally small cranium",
      "Decreased size of head",
      "Decreased size of skull",
      "Abnormally small head",
      "Small head",
      "small calvarium",
      "Small skull"
    ],
    "type": "Phenotype"
  }
]