Chembl molecule search

Skill ma-compbio-lab/SkillFoundry/skills/drug-discovery-and-cheminformatics/chembl-molecule-search

Use this skill to search ChEMBL molecules by keyword and return a compact compound summary. Do not use it for local chemistry calculations or unsupported bulk export.From its SKILL.md

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill chembl-molecule-search

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

2.3 KB, 497 tokens by cl100k_base, as published. Nobody here has run it

Purpose

Search ChEMBL by free-text query and return compact compound summaries suitable for quick cheminformatics triage.

When to use

You need a ChEMBL identifier and basic compound summary for a known drug or molecule name.
You want a lightweight compound lookup before deeper cheminformatics or screening workflows.

When not to use

You need local descriptor calculation or docking.
You need bulk export of a large ChEMBL slice.
You need offline execution.

Inputs

Query string
Optional result limit and output path

Outputs

JSON payload with query metadata and compact molecule summaries

Requirements

Python 3.10+
Network access to www.ebi.ac.uk

Procedure

Run python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1 --out skills/drug-discovery-and-cheminformatics/chembl-molecule-search/assets/chembl_imatinib.json.
Inspect molecules for chembl_id, preferred_name, molecule_type, max_phase, canonical_smiles, and selected properties.
Use the returned ChEMBL IDs in downstream compound-knowledge workflows when needed.

Validation

Command exits successfully.
molecules contains at least one ChEMBL result for a known query.
The first result has a non-empty chembl_id and molecule summary fields.

Failure modes and fixes

No hits: refine the query or use a more canonical drug name.
Too many hits: lower --limit and inspect the top results manually.
HTTP errors: retry later and keep the query simple for smoke verification.

Safety and limits

Knowledge lookup only.
This skill does not perform synthesis planning, structure optimization, or wet-lab decision making.

Example

python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1

Provenance

ChEMBL web services docs: https://www.ebi.ac.uk/chembl/api/data/docs
ChEMBL API base path: https://www.ebi.ac.uk/chembl/api/data/

Related skills

clinicaltrials-study-search

What ships with it: 9 files

13.4 KB alongside SKILL.md, 2 of them executable

assets/