How do I install the Chembl Query skill?

Run npx skillmds@latest add gabrielmoreira/chembl-query in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Chembl Query safe to use?

This skill has not completed SkillMD's automated safety review yet. Independent scanners report: SkillSpector: PASS, Skill Scanner: PASS. Capability flags: executes scripts, makes network calls. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Chembl Query?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Chembl Query free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Chembl Query?

gabrielmoreira (@gabrielmoreira) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Chembl Query by gabrielmoreira — Agent Skill

Name: Chembl Query
Rating: 4.2 (5 reviews)
Author: gabrielmoreira

Chembl Query

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.

gabrielmoreira Updated Sep 9, 2026 17 repo stars

File contents

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

---name: chembl-querydescription: 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.--- # 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: 1. **Single molecule by ID** — `query_molecules("CHEMBL25")` 2. **Batch molecule search by name** — `query_molecules(["ibuprofen", "metformin"], limit=3)` 3. **Bioactivities for multiple molecules** — `query_bioactivities(["CHEMBL25", "CHEMBL1642"], limit=3)` 4. **Single target by gene name** — `query_targets("EGFR", limit=3)` 5. **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

Frequently asked questions