Bad identifier: PI3-kinase p110-delta subunit inhibitor

[dkoslicki]

If you look up PI3-kinase p110-delta subunit inhibitor on the node synonymizer, you'll see that it has the identifier CHEMBL.MECHANISM:pi3-kinase_p110-delta_subunit_inhibitor. This is related to: https://github.com/NCATSTranslator/Feedback/issues/1039

This will likely become a non-issue after moving to NodeNorm, but in case you wanted to fix this

[saramsey]

Looks like the KG2pre build system currently hardcodes NamedThing for these:

RTX-KG2/convert/chembl_mysql_to_kg_jsonl.py

Line 283 in 2261c0f

category_label = kg2_util.BIOLINK_CATEGORY_NAMED_THING

[saramsey]

I'm going to transfer this issue to RTX-KG2

[saramsey]

Apparently, this concept name doesn't resolve, at least, not via the SRI Name Resolver. This request

curl -X 'GET' \
  'https://name-lookup.ci.transltr.io/lookup?string=pi3-kinase_p110-delta_subunit_inhibitor&autocomplete=true&highlighting=false&offset=0&limit=10' \
  -H 'accept: application/json'

produces the following null result:

 []

As a positive control, this query:

curl -X 'GET' \
  'https://name-lookup.ci.transltr.io/lookup?string=paracetamol&autocomplete=true&highlighting=false&offset=0&limit=10' \
  -H 'accept: application/json'

produces a ton of CURIEs, of which I enclose an excerpt below:

[
  {
    "curie": "CHEBI:32635",
    "label": "paracetamol sulfate",
    "highlighting": {},
    "synonyms": [
      "CHEMBL3544802",
      "paracetamol sulfate",
      "Paracetamol sulfate",
      "Paracetamol sulphate",
      "Acetaminophen-sulfate",
      "ACETAMINOPHEN SULFATE",

[saramsey]

I think if we can't get a controlled vocabulary ID out of ChEMBL mechanisms, we may want to drop it from the ChEMBL ETL.