monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
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Add heritability data for mondo diseases #295

Closed kevinschaper closed 1 year ago

kevinschaper commented 2 years ago

I'm not sure where this info comes from (it doesn't appear to come in with mondo nodes), or how we'll model it in biolink, but currently in the /bioentity/disease/{id} call in the biolink-api this inheritance section is returned for a disease, and we'll need to support that:

"inheritance": [
    {
      "id": "HP:0000006",
      "label": "Autosomal dominant inheritance",
      "iri": "http://purl.obolibrary.org/obo/HP_0000006",
      "category": [
        "inheritance"
      ]
    }
  ],

For example, accessing Asperger syndrome, X-linked, susceptibility to, 1 (MONDO:0010340) using /bioentity/disease/{id} call in the biolink-api, as noted above, gets back

{
  "inheritance": [
    {
      "id": "HP:0001426",
      "label": "Multifactorial inheritance",
      "iri": "http://purl.obolibrary.org/obo/HP_0001426",
      "category": [
        "inheritance"
      ]
    },
    {
      "id": "HP:0001417",
      "label": "X-linked inheritance",
      "iri": "http://purl.obolibrary.org/obo/HP_0001417",
      "category": [
        "inheritance"
      ]
    },
    {
      "id": "HP:0001425",
      "label": "Heterogeneous",
      "iri": "http://purl.obolibrary.org/obo/HP_0001425",
      "category": [
        "inheritance"
      ]
    },
    {
      "id": "HP:0003745",
      "label": "Sporadic",
      "iri": "http://purl.obolibrary.org/obo/HP_0003745",
      "category": [
        "inheritance"
      ]
    }
  ],
etc...
RichardBruskiewich commented 2 years ago

The Biolink Model does have a biolink:inheritance model defined, which is likely generally aligned with this issue. However, upon scrutiny, one suspected the need to trigger a fresh cycle of review and possible model revisions, see PR https://github.com/biolink/biolink-model/issues/1064.

kevinschaper commented 1 year ago

This is done