Medication -> Compound/Substance i.e. rxnorm -> pubchem -> chembl

bwalsh commented 2 years ago

Currently, a medication is expressed as follows:

          "coding": [
            {
              "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
              "code": "834102",
              "display": "Penicillin V Potassium 500 MG Oral Tablet"
            }
          ],

In order to enable clinical predictions we need to link to drug response and other evidence in bmeg and other knowledgebases. This means we will need to append key(s) from pubchem:

            {
              "system": "https://pubchem.ncbi.nlm.nih.gov/compound",
              "code": "6869",
              "display": "Penicillin V"
            },
            {
              "system": "https://pubchem.ncbi.nlm.nih.gov/compound",
              "code": "5462222",
              "display": "Potassium"
            }

The RXCUI https://pubchem.ncbi.nlm.nih.gov/source/25200 may be useful ? Or, chaining through SNOMED. https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F56723006 ?

bwalsh commented 1 year ago

Jordan Lee Yesterday at 2:54 PM might be useful for rxnorm conversion to chembl https://think-lab.github.io/d/40/

brian 10 minutes ago Part of a very interesting paper https://think-lab.github.io/p/rephetio/

brian 9 minutes ago https://neo4j.het.io/browser/

https://think-lab.github.io/d/61/

bwalsh commented 1 year ago

wiki data links https://www.wikidata.org/wiki/Q57055

ACED-IDP / data_model

Medication -> Compound/Substance i.e. rxnorm -> pubchem -> chembl #19