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.
Install
$ agentstack add skill-ma-compbio-lab-skillfoundry-chembl-molecule-search ✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.
Security review
✓ PassedNo issues found. Passed automated security review. · v0.1.0 How review works →
- ✓ Prompt-injection patterns
- ✓ Secret / credential exfiltration
- ✓ Dangerous shell & filesystem operations
- ✓ Untrusted network calls
- ✓ Known-malicious package signatures
What it can access
- ✓ Network access No
- ✓ Filesystem access No
- ✓ Shell / process execution No
- ✓ Environment & secrets No
- ✓ Dynamic code execution No
From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.
Verified badge
Passed review? Show it. Paste this badge into your README, it links to the public security report.
Links to your public security report.[](https://agentstack.voostack.com/security/report/skill-ma-compbio-lab-skillfoundry-chembl-molecule-search) Reliability & compatibility
Declared compatibility
Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.
We're building live execution health for every listing: tool-call success rate, median latency, uptime, and last-checked timestamps, measured, not self-reported. It isn't live yet, so we don't show numbers we can't stand behind.
How agent discovery & health will work →About
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
moleculesforchembl_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.
moleculescontains at least one ChEMBL result for a known query.- The first result has a non-empty
chembl_idand molecule summary fields.
Failure modes and fixes
- No hits: refine the query or use a more canonical drug name.
- Too many hits: lower
--limitand 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
Source & license
This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.
- Author: ma-compbio-lab
- Source: ma-compbio-lab/SkillFoundry
- License: Apache-2.0
- Homepage: https://ma-compbio-lab.github.io/SkillFoundry/
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.