ChEBI Query Skill

Search the ChEBI 2.0 REST API by any entity. Auto-detects input type:

Input Pattern	Detected As	Action
CHEBI:15422 / chebi:15422	ChEBI ID (prefixed)	full entity lookup via /compound/{id}/
27732 (pure digits ≤7)	ChEBI ID (numeric)	full entity lookup via /compound/{id}/
anything else	free text	Elasticsearch search via /es_search/?term=...

API

Function	Input	Returns
search(query, max_results=25)	single entity string	list[dict]
search_batch(queries, max_results=25)	list of entity strings	dict[str, list[dict]]
summarize(results, label)	result list + label	compact one-line-per-hit text
to_json(results)	result list	list[dict] (JSON-serialisable)

Lower-level helpers (called internally):

Function	Purpose
search_chebi(query, max_results)	keyword search via GET /es_search/?term=...&size=N
get_entity(chebi_id)	full entity via GET /compound/CHEBI:{id}/
get_entities_batch(chebi_ids)	batch lookup via GET /compounds/?chebi_ids=id1,id2,...

search_batch() automatically uses the efficient batch endpoint when all queries are ChEBI IDs; otherwise it iterates with a 0.3 s delay.

Usage

See if __name__ == "__main__" block in 64_ChEBI.py for runnable examples covering: single ID lookup, name search, formula search, batch ID search, mixed batch search, and JSON output.

Key Fields Returned

Top-level: chebi_accession, name, ascii_name, definition, stars (curation quality; 3 = fully curated), secondary_ids, is_released.

chemical_data (nested dict): formula, charge, mass, monoisotopic_mass.

default_structure (nested dict): smiles, standard_inchi, standard_inchi_key, wurcs.

names (nested dict by type): keys like IUPAC NAME, SYNONYM, BRAND NAME, UNIPROT NAME; each value is a list of name objects.

ontology_relations: incoming_relations and outgoing_relations, each a list of {init_id, init_name, relation_type, final_id, final_name}.

database_accessions (nested dict by type): CAS, MANUAL_X_REF, REGISTRY_NUMBER, CITATION; cross-refs to DrugBank, KEGG, HMDB, PubChem, PDBeChem, Wikipedia, etc.

roles_classification: list of role dicts with chebi_accession, name, definition, biological_role (bool), application (bool), chemical_role (bool).

Data Source

• Database: ChEBI 2.0 (EMBL-EBI), >195,000 molecular entities
• API base: https://www.ebi.ac.uk/chebi/backend/api/public/
• Docs: https://www.ebi.ac.uk/chebi/backend/api/docs/
• License: CC BY 4.0
• Citation: Bento et al. Nucleic Acids Res. 2025, 54(D1), D1768–D1774.