ChEBI
ChEBI (Chemical Entities of Biological Interest) is a curated dictionary and ontology of small molecules maintained by EMBL-EBI. In ScholarMuse it is an add-on to compound lookup: after a compound is found in PubChem, the tool looks for the ChEBI entry with the same InChIKey or name and attaches its id, definition and roles. ChEBI cannot be searched on its own here.
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 ChEBI.
lookup_compound
These fields sit inside the nested chebi object of the PubChem record, and only when a ChEBI entry matches.
- chebiId
- ChEBI accession, e.g. CHEBI:27732
- name
- ChEBI name of the entity
- definition
- ChEBI text definition, up to 2,000 characters
- stars
- ChEBI star rating of the entry
- roles
- Role names from the ChEBI classification, up to 12
- url
- Link to the ChEBI entry page
- license
- Licence of the ChEBI part of the record
- attribution
- Attribution text for the ChEBI part
What it covers
- ChEBI entries for compounds that are also in PubChem, one entry per compound lookup.
- Matching is strict: the entry must have the same InChIKey as the PubChem compound, or failing that exactly the same name.
- Returned content: ChEBI id, name, definition, star rating and role names.
Limits
- ChEBI cannot be searched directly. You cannot pass a ChEBI id, and entities that have no PubChem compound cannot be reached.
- Only the top 5 ChEBI search hits are checked for a match, so some compounds come back without ChEBI data.
- The ontology itself is not returned: no parent or child classes, no relationships, and roles are names without their ChEBI ids.
- If the ChEBI request fails, the PubChem record is still returned and the response is marked partial.
How ScholarMuse reaches ChEBI
After PubChem returns a compound, the connector calls the ChEBI 2.0 public REST API at ebi.ac.uk: the es_search endpoint to find the entry, then the compound endpoint for its details. No API key is sent.
Responses are cached for up to 7 days, so edits to a ChEBI entry 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: CC BY 4.0
Data from ChEBI (www.ebi.ac.uk/chebi), EMBL-EBI, CC BY 4.0.
The record itself is stamped with PubChem’s licence. The ChEBI licence and this line sit inside the nested chebi object. When you cite the data in a paper, follow ChEBI's own citation guidance.
