ingest SIDER for hackathon for KS

[realmarcin]

No description provided.

[andrewsu]

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]

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]

?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 | [email protected] | https://robinsongroup.github.io/ Peter Robinson

________________________________ From: Chris Mungall <[email protected]> Sent: Wednesday, April 18, 2018 3:41 PM To: NCATS-Tangerine/translator-knowledge-graph Cc: Peter Robinson; Mention Subject: Re: [NCATS-Tangerine/translator-knowledge-graph] ingest SIDER for hackathon for KS (#3) Nice, I think the mapping to ontology terms should be straightforward. @pnrobinson<https://github.com/pnrobinson> or @drseb<https://github.com/drseb> is there anything of your work we can reuse here? - You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#3 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AEtuPGuhatakwlsE4DFBCLzDqetyg8p6ks5tp5bVgaJpZM4Tam5p>. --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

[cmungall]

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