PubChem Compound Search

Overview

PubChem (NCBI) is the largest freely available chemical database — 110M+ compounds, 280M+ substances, and millions of bioassay records. Its PUG-REST JSON API is the canonical programmatic surface, and every example here uses it directly via plain requests. The Python pubchempy wrapper is not required; the PUG-REST URL grammar is small enough that direct calls are more transparent, easier to retry/cache, and avoid sandbox dependency issues (the library is not in TOOL_STATUS.md).

The URL pattern is fixed and predictable:

https://pubchem.ncbi.nlm.nih.gov/rest/pug/<input>/<operation>/<output>

• <input> = compound/{name,cid,smiles,inchikey,formula}/<value>
• <operation> = cids, property/<list>, synonyms, description, assaysummary, JSON (full record), SDF, PNG
• <output> = JSON, CSV, TXT, SDF, PNG

For long-running operations (similarity, substructure, formula) the API returns HTTP 202 + {"Waiting": {"ListKey": "..."}}; poll compound/listkey/{key}/cids/JSON until it returns IdentifierList. The skill handles this pattern in Module 4.

When to Use