Chembl

Skill BioTender-max/awesome-bio-agent-skills/skills/drugclaw/chembl

Query the ChEMBL database for drug molecules, bioactivity data, and drug targets via the ChEMBL REST API. Use whenever the user asks about drug properties (molecular weight, logP, Lipinski violations), drug-target interactions, bioactivity assay results, or wants to look up any entity by ChEMBL ID or drug/gene name in ChEMBL. Supports single entity or batch queries. No API key required.From its SKILL.md

Install

npx -y skills add BioTender-max/awesome-bio-agent-skills --skill chembl

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SKILL.md

2.5 KB, 622 tokens by cl100k_base, as published. Nobody here has run it

ChEMBL Query Skill

Query ChEMBL bioactivity database for molecules, targets, and activity data. Auto-detects input type by prefix:

Input Pattern	Detected As	Action
`CHEMBL25`	ChEMBL ID (molecule)	direct fetch by ID
`aspirin`	drug name	substring search on `pref_name`
`CHEMBL203`	ChEMBL ID (target)	direct fetch by ID
`EGFR`	gene/protein name	substring search on `target_synonym`

API

Function	Input	Returns
`query_molecules(entities, limit)`	`str` or `list[str]` — ChEMBL IDs or drug names	`dict[str, list[dict]]`
`query_targets(entities, limit)`	`str` or `list[str]` — ChEMBL IDs or gene names	`dict[str, list[dict]]`
`query_bioactivities(chembl_ids, limit)`	`str` or `list[str]` — molecule ChEMBL IDs	`dict[str, list[dict]]`
`summarize_molecule(mol)`	single molecule dict	compact one-line string
`summarize_activity(act)`	single activity dict	compact one-line string
`summarize_target(tgt)`	single target dict	compact one-line string

Usage

See if __name__ == "__main__" block in chembl_query.py for runnable examples covering:

Single molecule by ID — query_molecules("CHEMBL25")
Batch molecule search by name — query_molecules(["ibuprofen", "metformin"], limit=3)
Bioactivities for multiple molecules — query_bioactivities(["CHEMBL25", "CHEMBL1642"], limit=3)
Single target by gene name — query_targets("EGFR", limit=3)
Batch target lookup by ID — query_targets(["CHEMBL203", "CHEMBL204"])

Key Fields

Molecule: molecule_chembl_id, pref_name, molecule_properties.full_mwt, molecule_properties.alogp, molecule_properties.num_ro5_violations

Activity: molecule_chembl_id, target_chembl_id, target_pref_name, standard_type, standard_value, standard_units

Target: target_chembl_id, pref_name, target_type, organism

Data Source

API: https://www.ebi.ac.uk/chembl/api/data (no key required)
Paper: https://doi.org/10.1093/nar/gkad1004

What ships with it: 5 files

21.5 KB alongside SKILL.md, 4 of them executable

chembl_skill.pyruns11.3 KB
example.pyruns7.5 KB
__init__.pyruns130 B
README.md1.1 KB
retrieve.pyruns1.5 KB