Add Disease Ontology as a new resource for MyDisease.info

Download: https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/master/src/ontology

Steps:

_id

MyDisease.info use MONDO as the default primary id (_id)
- If DOID - MONDO mapping available, use MONDO as _id
  - use batch query feature in MyDisease.info to do the mapping
  - query for "mondo.xrefs.doid" for the DOID, and retrieve "_id" from mydisease.info
- otherwise, use DOID instead
Fields to extract
- exact synonyms, type list
- related synonyms, type list
- is a, maybe a list (need to loop through the whole document to make sure), map to "parents" in mydisease.info
- xrefs (type list)
- for how to restructure xrefs, refer here
- name (string)
- definition (string)
- doid (string)
Output structure

{
  "_id": "MONDO:12344",
  "disease_ontology": {
     "doid": "DOID:0111648",
     "name": "ectopia lentis with ectopia of pupil",
     "definition": "An eye disease characterized by displacement of the lenses and the pupils in association with other ocular anomalies that has_material_basis_in homozygous or compound heterozygous mutation mutation in ADAMTSL4 on chromosome 1q21.2.",
    "synonyms": {
        "exact": ["..."],
        "related": ["..."]
    },
    "xrefs": {
        "mesh": "D...",
        "ncit": "...",
    },
    "parents": ["DOID:0050737", "DOID:5614"],

biothings / mydisease.info

Add Disease Ontology as a new resource for MyDisease.info #15