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Discuss BindingDB issues: related to parser / API? #99

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colleenXu opened this issue Dec 21, 2022 · 3 comments
Closed

Discuss BindingDB issues: related to parser / API? #99

colleenXu opened this issue Dec 21, 2022 · 3 comments
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data source Data source pending to create a new API

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@colleenXu
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Related to biothings/biothings_explorer#532 (comment)

  • looking at the bindingdb website, we may be able to pick a more specific relationship for a chemical-gene pair
    • can we get the assay description and find keywords in that text? For example, the assay description for this pair seems to say this chem is an agonist of this gene...
    • can we use the existence of certain fields + the values of those fields? For example, if the IC50 field exists and its value is small, maybe this chem is an inhibitor of this gene.
      • The Ki field existence and value can maybe used as well. I'm not sure if other fields can be used.
      • the values are tricky because some are integers, some are floats, and some are integers ">40000"
  • info: see my old note here, listing fields here, bindingDB's info
@andrewsu andrewsu added the data source Data source pending to create a new API label Aug 22, 2023
@andrewsu andrewsu changed the title Update BindingDB? Update BindingDB smartAPI annotation Aug 22, 2023
@colleenXu colleenXu changed the title Update BindingDB smartAPI annotation Discuss BindingDB issues: related to parser / API? Sep 2, 2023
@colleenXu
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colleenXu commented Sep 2, 2023

There's at least 3 ID fields in our BioThings BindingDB API, where values sometimes seem incorrect:

  • object.pubchem_cid
  • object.inchikey
  • object.chembl
`object.pubchem_cid` examples

`object.inchikey` examples

`object.chembl` examples

(Thanks to Andy Crouse from Translator's UI team (Translator Slack link) for pointing out the pubchem cid problem)

@colleenXu
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colleenXu commented Sep 2, 2023

For now, I've changed the x-bte annotation for this resource NCATS-Tangerine/translator-api-registry@022e876:

(1) Use object.inchikey:

  • covers a little over 96% of the resource (1394153 / 1438909)
  • my hunch is that the INCHIKEY IDs are not completely incorrect, VS the pubchem cids are sometimes incorrect and I don't really know why
  • VS object.pubchem_cid (used before) covers a little over 98% of the resource (1413051 / 1438909)
  • other fields cover much less of the resource or aren't supported by Node Norm:
    • object.pubchem_sid: 1413131 but Node Norm doesn't seem to support this ID namespace right now
    • object.chembl: 631745. Has its own issues, see last comment
    • object.kegg (KEGG.COMPOUND): 33680
    • object.chebi: 25903
    • object.drugbank: 24177

(2) Retrieve subject.name and object.name fields for input_name/output_name behavior, if Node Norm doesn't retrieve info for the ID. Every document has those fields, but the names provided have issues (will be covered in a later post).

@colleenXu
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Going to close this issue, and replace with issues in the BTE repo

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