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HermannKroll / NarrativeIntelligence

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Narrative Service: additional PubChem information #189

Open ir0ntr0nik opened 1 year ago

ir0ntr0nik commented 1 year ago

Is there a way to retrieve the PubChem id from the ChemblApi Drug-Request. To be precise: does the data contain the id?

If not: is there any other way to retrieve this information via the API?

ir0ntr0nik commented 1 year ago

It is not directly possible to retrive the PubChemID from the ChemblAPI request. The recommendation is to use the UniChem translation service. The response of the Chembl request contains the inchi(-key) which can be used for the translation.

Therefore, we need 3 (2 more than now) requests to get additional PubChem information: (example: metformin)

  1. ChemblAPI request: https://www.ebi.ac.uk/chembl/api/data/drug/CHEMBL1431.json -> inchikey (standard_inchi_key)
  2. UniChem translation request: https://www.ebi.ac.uk/unichem/rest/inchikey/XZWYZXLIPXDOLR-UHFFFAOYSA-N?format=json -> translated CID (translation idx number 22 for PubChemID, probably the lowest translated id?)
  3. PubChemAPI request: https://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/4091/JSON?heading=Experimental+Properties
HermannKroll commented 1 year ago

Experts need to specify a set of relevant properties: https://pubchem.ncbi.nlm.nih.gov/compound/54454