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Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling.
Passed 9 of 15 test cases with the skill, and 8 of 15 without it.
and 6 more in the full report
7 fixed8 passed either way4 still failing6 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 6 test cases the skill fixed. Same model, same prompt, with and without the skill.
When gathering bioactivity metrics for a small molecule, if ChEMBL returns no recorded compound activities, what primary fallback tool should be queried?
| Checked | Without skill | With skill |
|---|---|---|
| The response specifies falling back to PubChem BioAssay summary. | Missed | Passed |
The instructions your model reads when the skill loads.
Retrieve comprehensive chemical compound data with proper disambiguation and cross-database validation.
LOOK UP DON'T GUESS: Never assume a CID, ChEMBL ID, or molecular property value. Always retrieve from PubChem/ChEMBL.
English-first: Always use English compound names in tool calls. Respond in user's language.
"Aspirin" = one compound. "Vitamin D" = multiple forms (D2/D3/active metabolite). For generic class names (steroids, vitamins, acids), present candidates and confirm before proceeding.
Phase 0: Clarify (only if highly ambiguous -- skip for unambiguous names or specific IDs)
Phase 1: Disambiguate → resolve PubChem CID + ChEMBL ID
Phase 2: Retrieve data (silent)
Phase 3: Report compound profile
# By name
result = tu.tools.PubChem_get_CID_by_compound_name(compound_name=name)
# By SYSTEMATIC (IUPAC) name -> structure, deterministic parser (no DB lookup)
opsin = tu.tools.OPSIN_name_to_structure(name="2-acetoxybenzoic acid")
# Returns {parsed, smiles, inchi, inchikey}; use the SMILES/InChIKey to anchor a
# PubChem_get_CID_by_SMILES lookup. Trade/trivial names give parsed=false -> fall
# back to PubChem_get_CID_by_compound_name for those.
# By SMILES
result = tu.tools.PubChem_get_CID_by_SMILES(smiles=smiles)
# Cross-reference
chembl_result = tu.tools.ChEMBL_search_molecules(query=name, limit=5)
Verify: CID + ChEMBL ID + canonical SMILES + stereochemistry + salt forms.
test cases passed, vs 8 / 15 without
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