caseyta / cohd Goto Github PK

Not sure if this is the right place to report...

I'm using http://smart-api.info/ui/?url=/api/metadata/6c33ed14d628a982c79fa36a75dbbbcf, very clear API thanks

I'm trying to find additional info on each concept in particular the diseases, it looks like the IDs assigned are local to this particular dataset. E.g. http://cohd.nsides.io/api/v1/omop/concepts?q=192855

{
  "results": [
    {
      "concept_id": 192855,
      "concept_name": "Cancer in situ of urinary bladder",
      "domain_id": "Condition"
    }
  ]
}

The ID 192855 doesn't seem to correspond to any vocabulary I know. My guess is that this came from snomed as AFAIK it is the only vocabulary that uses "cancer in situ" as a synonym for "carcinoma in situ". The snomed ID for this is SCTID:92546004 which doesn't seem to be linked (or NCIT:C3644 or UMLS:C0154091 or ICD10:D09.0 ...).

I would be interested in using this API at the translator meeting next week. If no such mapping exists I can create a reasonably accurate one quickly (if you can provide a dump of all concepts that would be easier than me iterating through the API). Or if the mapping exists, would it be possible to expose this (just a file is fine - I can help expose via either this API, or via a separate API that uses our MONDO resource).

Could you check the example notebook for the API. I think it's broken and there seems to be no way obvious way to load it anywhere.