ingest SIDER for hackathon for KS

andrewsu commented 6 years ago

FYI, looks like mychem.info ingests SIDER. Example query:

http://mychem.info/v1/chem/KWHRDNMACVLHCE-UHFFFAOYSA-N

{
  "_id": "KWHRDNMACVLHCE-UHFFFAOYSA-N",
  "_version": 1,
  "pubchem": {
    ...
  },
  "sider": [
    {
      "_license": "https://goo.gl/8b7ZCQ",
      "meddra": {
        "type": "LLT",
        "umls_id": "C0042029"
      },
      "side_effect": {
        "frequency": "0.448%",
        "name": "Urinary tract infection",
        "placebo": false
      },
      "stitch": {
        "flat": "CID116156130",
        "stereo": "CID016157882"
      }
    },
    {
      "_license": "https://goo.gl/8b7ZCQ",
      "meddra": {
        "type": "PT",
        "umls_id": "C0041912"
      },
      "side_effect": {
        "frequency": "9.04%",
        "name": "Upper respiratory tract infection",
        "placebo": false
      },
      "stitch": {
        "flat": "CID116156130",
        "stereo": "CID016157882"
      }
    },
    ...
}

To query by drugname: http://mychem.info/v1/query?q=drugbank.name:imatinib To query by drugbank ID: http://mychem.info/v1/query?q=drugbank.drugbank_id:DB02968

cmungall commented 6 years ago

Nice, I think the mapping to ontology terms should be straightforward. @pnrobinson or @drseb is there anything of your work we can reuse here?

pnrobinson commented 6 years ago

?SIDER is using UMLS, which is mapped to HPO. We had our own mapping years ago, but I would suggest just using and evaluating the UMLS to HPO mapping. Last time I looked, about 5% of the data in SIDR was erroneous, and so additional curation might be needed for medical use.

-Peter

Peter Robinson Professor and Donald A. Roux Chair, Genomics and Computational Biology The Jackson Laboratory for Genomic Medicine 860.837.2095 t | 860.990.3130 m | peter.robinson@jax.org | https://robinsongroup.github.io/ Peter Robinson

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Nice, I think the mapping to ontology terms should be straightforward. @pnrobinsonhttps://github.com/pnrobinson or @drsebhttps://github.com/drseb is there anything of your work we can reuse here?

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cmungall commented 6 years ago

I would suggest just using and evaluating the UMLS to HPO mapping

good point. We can also use UMLS to MONDO, since some of these will more clearly map to disease entities?

Last time I looked, about 5% of the data in SIDR was erroneous, and so additional curation might be needed for medical use

I believe the use case here will tolerate this as it's statistical and no one will actually be making clinical recommendations. But it is good to know these stats, build them in as priors etc

NCATS-Tangerine / translator-knowledge-graph

ingest SIDER for hackathon for KS #3