PubChem
PubChem is the open chemistry database of the U.S. National Library of Medicine at the NIH. Through ScholarMuse, an agent can resolve a compound name, CAS number, SMILES string, InChIKey or CID to one PubChem compound and read its identifiers and computed properties, so it does not have to recall chemical facts from memory. When ChEBI has a matching entry, its definition and roles are added.
ScholarMuse tools: lookup_compound. Each successful call uses credits.
Ask your agent
What your agent gets back
Every record carries id, source, title, url, license, attribution and retrievedAt. The fields below are the data that comes from PubChem.
lookup_compound
All fields below come from PubChem. A nested chebi object is added only when ChEBI has a matching entry.
- cid
- PubChem compound id
- name
- PubChem title of the compound
- iupacName
- IUPAC name
- formula
- Molecular formula
- molecularWeight
- Molecular weight in g/mol
- smiles
- SMILES string
- inchiKey
- InChIKey
- xlogp
- Computed XLogP
- hBondDonors
- Hydrogen bond donor count
- hBondAcceptors
- Hydrogen bond acceptor count
- tpsa
- Topological polar surface area
- casNumber
- CAS number, when found among the synonyms
What it covers
- PubChem Compound records, one compound per call.
- Accepted inputs: compound name, CAS number, SMILES, InChIKey or CID.
- Identifiers and computed properties, the first 8 synonyms, and a link to the 2D structure image (imageUrl).
Limits
- One compound per call. When a name matches several CIDs, the first one PubChem returns is used. There is no list search.
- No substructure or similarity search, bioassay results, safety and hazard data, spectra, 3D conformers or experimental properties such as melting point.
- Property values such as XLogP and TPSA are PubChem computed values, not measurements.
- The query can be at most 400 characters long.
How ScholarMuse reaches PubChem
The connector calls PubChem PUG REST: it resolves the query to a CID by name, SMILES or InChIKey, then reads the property table and the synonym list for that CID. No API key is sent.
Responses are cached for up to 30 days, so very recent changes at PubChem can take that long to appear.
API key: the upstream API can be called without one, so you do not add one.
Licence and attribution
Licence: Public domain (US Government work); depositor-supplied items may carry their own terms
Data from PubChem (pubchem.ncbi.nlm.nih.gov), National Library of Medicine, NIH.
Records that come from PubChem carry this licence and attribution. When you cite the data in a paper, follow PubChem's own citation guidance.
