Chembl Database
Google DeepMindOfficialPublished by Google DeepMind
- Skill
- Tool integration
- Science and research
- Apache-2.0
- Low risk
- Has scripts
AutoGineer summary
Written by AutoGineer from the skill’s own files, not by the author
The ChEMBL database skill provides a structured interface to query the EBI ChEMBL database for information on bioactive molecules, drug targets, bioactivity data, and chemical structures. It utilizes a dedicated utility script to manage API interactions, ensuring rate limiting and error handling are managed correctly. The skill supports various operations including searching for molecules by name, fetching detailed target information, retrieving bioactivity data with unit normalization, and performing server-side structure-based searches like similarity and substructure matching.
What it does
- Fetches detailed information for molecules, targets, and approved drugs using ChEMBL IDs.
- Performs free-text searches for molecules, targets, and bioactivity data.
- Retrieves and normalizes bioactivity data (e.g., IC50, Ki) to nM units for consistent analysis.
- Executes server-side similarity and substructure searches using SMILES strings.
- Downloads 2D chemical structure images in SVG or PNG formats.
- Cross-references ChEMBL entities with external databases like UniProt.
When to use it
- When you need to retrieve bioactivity data for specific drug targets or compounds.
- When performing structure-based searches to find similar molecules or substructures.
- When investigating drug mechanisms of action or clinical indications.
- When you need to download chemical structure diagrams for research documentation.
- When mapping protein targets to UniProt accessions or other cross-references.
Advantages
- Ensures consistent API interaction through a centralized utility script.
- Supports server-side structure searching without requiring local cheminformatics software.
- Provides built-in unit normalization for bioactivity data.
- Enables easy integration with other tools by outputting results to JSON files.
- Facilitates batch processing and pagination for large datasets.
Usage examples
- “Find the target information for EGFR.”
- The agent uses the target search command to retrieve a list of EGFR-related targets and their corresponding ChEMBL IDs, saving the results to a JSON file.
- “Get all IC50 values for CHEMBL203 normalized to nM.”
- The agent queries the activity endpoint with filters for the target ID and standard type, applying the normalization flag to produce a file with consistent nM values.
- “Find molecules similar to aspirin (SMILES: CC(=O)Oc1ccccc1C(=O)O) with 85% similarity.”
- The agent executes a similarity search against the ChEMBL database and saves the matching molecules to a specified output file.
- “Download a 2D structure image for CHEMBL25.”
- The agent generates an SVG image file of the molecule structure for use in reports or presentations.
Install
Download the skill as a ZIP:
https://mp-staging.autogineer.com/agent-skills/google-deepmind/chembl-database/downloadUnzip it into the cross-client skills folder of your project:
mkdir -p .agents/skills && unzip chembl-database.zip -d .agents/skills
Documentation by Google DeepMind
ChEMBL Database Query
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.User Notification: If .licenses/chembl_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://chembl.gitbook.io/chembl-interface-documentation/about, then (2) create the file recording the notification text and timestamp.
Core Rules
[!IMPORTANT] Use the Utility Scripts: You MUST ALWAYS use the provided utility script
scripts/chembl_api.pyfor all ChEMBL API interactions, including checking status. NEVER usecurlor custom Python requests to query the ChEMBL API directly. This ensures rate limit is enfoced and also retries on network errors.Output to File (Required): The
--outputflag is required for every subcommand. All JSON results are written to the specified file. After running the command, read the output file with jq or your own code to extract the data. List results are typically wrapped in a JSON array keyed by the endpoint name (e.g.,molecules,activities).Notification: If this skill is used, ensure this is mentioned in the output.
Utility Script
All ChEMBL API queries use one script with subcommands:
uv run scripts/chembl_api.py <subcommand> --output <file> [options]1. Check API Status
uv run scripts/chembl_api.py status --output /tmp/status.json2. Molecule Queries
Fetch by ChEMBL ID: bash uv run scripts/chembl_api.py molecule --id CHEMBL25 --output /tmp/mol.json
Search by name: bash uv run scripts/chembl_api.py molecule --search "aspirin" --limit 3 --output /tmp/mol_search.json
Batch fetch: bash uv run scripts/chembl_api.py molecule --ids "CHEMBL25;CHEMBL1642" --limit 10 --output /tmp/mol_batch.json
Filter by properties: bash uv run scripts/chembl_api.py molecule --filter molecule_properties__mw_freebase__lte=500 --limit 5 --output /tmp/mol_filter.json
Filter by range: bash uv run scripts/chembl_api.py molecule --filter molecule_properties__mw_freebase__range=150,200 --limit 5 --output /tmp/mol_range.json
Download SDF structure file: bash uv run scripts/chembl_api.py molecule --id CHEMBL25 --dl_format sdf --output /tmp/aspirin.sdf
Tip: SDF/MOL files can be passed directly to tools like PyMOL or RDKit for 3D visualization and analysis.
3. Target Queries
Search for targets: bash uv run scripts/chembl_api.py target --search "EGFR" --limit 5 --output /tmp/targets.json
Fetch by ID: bash uv run scripts/chembl_api.py target --id CHEMBL203 --output /tmp/egfr.json
4. Bioactivity Data
Fetch activity by ID: bash uv run scripts/chembl_api.py activity --id 31863 --output /tmp/act.json
Search activities: bash uv run scripts/chembl_api.py activity --search "EGFR" --limit 5 --output /tmp/act_search.json
Filter activities for a target: bash uv run scripts/chembl_api.py activity --filter target_chembl_id=CHEMBL203 standard_type=IC50 --limit 10 --output /tmp/egfr_ic50.json
Normalize bioactivity units to nM: bash uv run scripts/chembl_api.py activity --filter target_chembl_id=CHEMBL203 standard_type=IC50 --limit 5 --normalize --output /tmp/egfr_normalized.json
Important: Bioactivity values come in various units (nM, µM, pM). Use
--normalizeto convert all values to nM for consistent comparison. Each record will includenormalized_value_nMandnormalization_note.
5. Drug Information
Fetch drug details: bash uv run scripts/chembl_api.py drug --id CHEMBL25 --output /tmp/drug.json
Drug indications: bash uv run scripts/chembl_api.py drug_indication --filter molecule_chembl_id=CHEMBL25 --limit 10 --output /tmp/indications.json
Filter indications by phase: bash uv run scripts/chembl_api.py drug_indication --filter molecule_chembl_id=CHEMBL25 max_phase_for_ind=4.0 --limit 10 --output /tmp/approved_indications.json
Drug warnings: bash uv run scripts/chembl_api.py drug_warning --limit 5 --output /tmp/warnings.json
Mechanisms of action: bash uv run scripts/chembl_api.py mechanism --filter molecule_chembl_id=CHEMBL25 --limit 5 --output /tmp/mech.json
6. Structure-Based Searches
Note: Both similarity and substructure searches are performed server-side on ChEMBL's pre-indexed database. They do not require a local RDKit installation.
Similarity search (SMILES + threshold): bash uv run scripts/chembl_api.py similarity --smiles "CC(=O)Oc1ccccc1C(=O)O" --similarity 85 --limit 5 --output /tmp/similar.json
Substructure search (SMILES): bash uv run scripts/chembl_api.py substructure --smiles "c1ccccc1" --limit 5 --output /tmp/substruct.json
7. Compound Image
Download a 2D structure image (SVG by default, scalable for publication):
uv run scripts/chembl_api.py image --id CHEMBL25 --output /tmp/chembl25.svgOptions:
--dimensions: Image size in pixels (max 500, default 500).--engine: Rendering engine (default: rdkit).--img_format: Output format —svg(default, vector) orpng(raster).
8. Cross-Referencing with Other Databases
ChEMBL integrates with UniProt, Ensembl, PubChem, and other databases. Common cross-referencing patterns:
Find a ChEMBL target from a UniProt accession: bash uv run scripts/chembl_api.py target --filter target_components__accession=P00533 --limit 5 --output /tmp/uniprot_target.json
Resolve any ChEMBL ID to its entity type: bash uv run scripts/chembl_api.py chembl_id_lookup --id CHEMBL203 --output /tmp/lookup.json
Look up cross-reference sources: bash uv run scripts/chembl_api.py xref_source --limit 10 --output /tmp/xrefs.json
Tip: Use the
target_componentendpoint to find UniProt accessions, gene names, and protein sequences for any ChEMBL target.
9. Pagination
All list endpoints support --limit and --offset for pagination:
# First page: 2 results starting at offset 0
uv run scripts/chembl_api.py molecule --limit 2 --offset 0 --output /tmp/page1.json
# Second page: next 2 results starting at offset 2
uv run scripts/chembl_api.py molecule --limit 2 --offset 2 --output /tmp/page2.jsonThe response includes page_meta with total_count, limit, offset, next,
and previous links. Use successive --offset values to page through large
result sets.
10. Other Endpoints
All remaining endpoints follow the same pattern:
uv run scripts/chembl_api.py <subcommand> --output <file> [--id ID | --ids ID1;ID2 | --search QUERY] [--limit N] [--offset N] [--filter KEY=VAL ...]Key subcommands at a glance:
molecule(searchable: true): Molecules/compounds — the primary entry pointtarget(searchable: true): Drug targets (proteins, organisms, etc.)activity(searchable: true): Bioactivity data (IC50, Ki, EC50, etc.)drug(searchable: false): Approved drugsmechanism(searchable: false): Mechanisms of actionassay(searchable: true): Assay descriptionssimilarity(searchable: false): Similarity search (special)substructure(searchable: false): Substructure search (special)image(searchable: false): Compound image download (special)
Full subcommand list:
activity_supp(searchable: false): Supplementary activity dataassay_class(searchable: false): Assay classificationsatc_class(searchable: false): ATC drug classificationsbinding_site(searchable: false): Binding site informationbiotherapeutic(searchable: false): Biotherapeutic moleculescell_line(searchable: false): Cell line detailschembl_id_lookup(searchable: true): ChEMBL ID resolutionchembl_release(searchable: false): Database release infocompound_record(searchable: false): Compound recordscompound_structural_alert(searchable: false): Structural alertsdocument(searchable: true): Literature documentsdocument_similarity(searchable: false): Document similaritydrug_indication(searchable: false): Drug indicationsdrug_warning(searchable: false): Drug safety warningsgo_slim(searchable: false): GO slim termsmetabolism(searchable: false): Metabolism datamolecule_form(searchable: false): Molecule forms (salts/parents)organism(searchable: false): Organismsprotein_classification(searchable: true): Protein classificationssource(searchable: false): Data sourcestarget_component(searchable: false): Target protein componentstarget_relation(searchable: false): Target relationshipstissue(searchable: false): Tissue typesxref_source(searchable: false): Cross-reference sourcesstatus(searchable: false): API status check (special)
Common Options
--output FILE: Required. Output file path for JSON results.--id ID: Fetch a single record by ID.--ids ID1;ID2;...: Batch fetch multiple records.--search QUERY: Free-text search (only for searchable endpoints, marked ✓).--limit N: Max results to return (default: 5).--offset N: Pagination offset.--filter KEY=VAL: Filter parameters (can specify multiple).--normalize: (activity only) Normalize values to nM.--dl_format sdf|mol: (molecule only) Download structure file.
Reference
API Endpoints Reference: See references/api_endpoints.md for the full list of endpoints and filter operators.
Workflow
Use
status --output /tmp/status.jsonto verify the API is available.Search for targets, molecules, or drugs using the relevant subcommand.
Read the output JSON file to extract IDs and data.
Use IDs from search results to fetch detailed records.
Query
activitywith filters to get bioactivity data for targets/molecules. Use--normalizewhen comparing values across studies.Use
similarityorsubstructurefor server-side structure-based queries.Download compound images with
imageor structure files withmolecule --dl_format sdf.Use
target --filter target_components__accession=<UniProt>to cross- reference with UniProt.
Files
- ATTRIBUTION.mdAdded by AutoGineer912 B
- LICENSELicence file added by AutoGineer11.1 KiB
- SKILL.md11.2 KiB
- references/api_endpoints.md2.8 KiB
- references/citation.bib3.6 KiB
- scripts/chembl_api.pyScript18.4 KiB
LICENSE
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
1. Definitions.
"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.
"Licensor" shall mean the copyright owner or entity authorized by
the copyright owner that is granting the License.
"Legal Entity" shall mean the union of the acting entity and all
other entities that control, are controlled by, or are under common
control with that entity. For the purposes of this definition,
"control" means (i) the power, direct or indirect, to cause the
direction or management of such entity, whether by contract or
otherwise, or (ii) ownership of fifty percent (50%) or more of the
outstanding shares, or (iii) beneficial ownership of such entity.
"You" (or "Your") shall mean an individual or Legal Entity
exercising permissions granted by this License.
"Source" form shall mean the preferred form for making modifications,
including but not limited to software source code, documentation
source, and configuration files.
"Object" form shall mean any form resulting from mechanical
transformation or translation of a Source form, including but
not limited to compiled object code, generated documentation,
and conversions to other media types.
"Work" shall mean the work of authorship, whether in Source or
Object form, made available under the License, as indicated by a
copyright notice that is included in or attached to the work
(an example is provided in the Appendix below).
"Derivative Works" shall mean any work, whether in Source or Object
form, that is based on (or derived from) the Work and for which the
editorial revisions, annotations, elaborations, or other modifications
represent, as a whole, an original work of authorship. For the purposes
of this License, Derivative Works shall not include works that remain
separable from, or merely link (or bind by name) to the interfaces of,
the Work and Derivative Works thereof.
"Contribution" shall mean any work of authorship, including
the original version of the Work and any modifications or additions
to that Work or Derivative Works thereof, that is intentionally
submitted to Licensor for inclusion in the Work by the copyright owner
or by an individual or Legal Entity authorized to submit on behalf of
the copyright owner. For the purposes of this definition, "submitted"
means any form of electronic, verbal, or written communication sent
to the Licensor or its representatives, including but not limited to
communication on electronic mailing lists, source code control systems,
and issue tracking systems that are managed by, or on behalf of, the
Licensor for the purpose of discussing and improving the Work, but
excluding communication that is conspicuously marked or otherwise
designated in writing by the copyright owner as "Not a Contribution."
"Contributor" shall mean Licensor and any individual or Legal Entity
on behalf of whom a Contribution has been received by Licensor and
subsequently incorporated within the Work.
2. Grant of Copyright License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
copyright license to reproduce, prepare Derivative Works of,
publicly display, publicly perform, sublicense, and distribute the
Work and such Derivative Works in Source or Object form.
3. Grant of Patent License. Subject to the terms and conditions of
this License, each Contributor hereby grants to You a perpetual,
worldwide, non-exclusive, no-charge, royalty-free, irrevocable
(except as stated in this section) patent license to make, have made,
use, offer to sell, sell, import, and otherwise transfer the Work,
where such license applies only to those patent claims licensable
by such Contributor that are necessarily infringed by their
Contribution(s) alone or by combination of their Contribution(s)
with the Work to which such Contribution(s) was submitted. If You
institute patent litigation against any entity (including a
cross-claim or counterclaim in a lawsuit) alleging that the Work
or a Contribution incorporated within the Work constitutes direct
or contributory patent infringement, then any patent licenses
granted to You under this License for that Work shall terminate
as of the date such litigation is filed.
4. Redistribution. You may reproduce and distribute copies of the
Work or Derivative Works thereof in any medium, with or without
modifications, and in Source or Object form, provided that You
meet the following conditions:
(a) You must give any other recipients of the Work or
Derivative Works a copy of this License; and
(b) You must cause any modified files to carry prominent notices
stating that You changed the files; and
(c) You must retain, in the Source form of any Derivative Works
that You distribute, all copyright, patent, trademark, and
attribution notices from the Source form of the Work,
excluding those notices that do not pertain to any part of
the Derivative Works; and
(d) If the Work includes a "NOTICE" text file as part of its
distribution, then any Derivative Works that You distribute must
include a readable copy of the attribution notices contained
within such NOTICE file, excluding those notices that do not
pertain to any part of the Derivative Works, in at least one
of the following places: within a NOTICE text file distributed
as part of the Derivative Works; within the Source form or
documentation, if provided along with the Derivative Works; or,
within a display generated by the Derivative Works, if and
wherever such third-party notices normally appear. The contents
of the NOTICE file are for informational purposes only and
do not modify the License. You may add Your own attribution
notices within Derivative Works that You distribute, alongside
or as an addendum to the NOTICE text from the Work, provided
that such additional attribution notices cannot be construed
as modifying the License.
You may add Your own copyright statement to Your modifications and
may provide additional or different license terms and conditions
for use, reproduction, or distribution of Your modifications, or
for any such Derivative Works as a whole, provided Your use,
reproduction, and distribution of the Work otherwise complies with
the conditions stated in this License.
5. Submission of Contributions. Unless You explicitly state otherwise,
any Contribution intentionally submitted for inclusion in the Work
by You to the Licensor shall be under the terms and conditions of
this License, without any additional terms or conditions.
Notwithstanding the above, nothing herein shall supersede or modify
the terms of any separate license agreement you may have executed
with Licensor regarding such Contributions.
6. Trademarks. This License does not grant permission to use the trade
names, trademarks, service marks, or product names of the Licensor,
except as required for reasonable and customary use in describing the
origin of the Work and reproducing the content of the NOTICE file.
7. Disclaimer of Warranty. Unless required by applicable law or
agreed to in writing, Licensor provides the Work (and each
Contributor provides its Contributions) on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
implied, including, without limitation, any warranties or conditions
of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
PARTICULAR PURPOSE. You are solely responsible for determining the
appropriateness of using or redistributing the Work and assume any
risks associated with Your exercise of permissions under this License.
8. Limitation of Liability. In no event and under no legal theory,
whether in tort (including negligence), contract, or otherwise,
unless required by applicable law (such as deliberate and grossly
negligent acts) or agreed to in writing, shall any Contributor be
liable to You for damages, including any direct, indirect, special,
incidental, or consequential damages of any character arising as a
result of this License or out of the use or inability to use the
Work (including but not limited to damages for loss of goodwill,
work stoppage, computer failure or malfunction, or any and all
other commercial damages or losses), even if such Contributor
has been advised of the possibility of such damages.
9. Accepting Warranty or Additional Liability. While redistributing
the Work or Derivative Works thereof, You may choose to offer,
and charge a fee for, acceptance of support, warranty, indemnity,
or other liability obligations and/or rights consistent with this
License. However, in accepting such obligations, You may act only
on Your own behalf and on Your sole responsibility, not on behalf
of any other Contributor, and only if You agree to indemnify,
defend, and hold each Contributor harmless for any liability
incurred by, or claims asserted against, such Contributor by reason
of your accepting any such warranty or additional liability.
END OF TERMS AND CONDITIONS
APPENDIX: How to apply the Apache License to your work.
To apply the Apache License to your work, attach the following
boilerplate notice, with the fields enclosed by brackets "[]"
replaced with your own identifying information. (Don't include
the brackets!) The text should be enclosed in the appropriate
comment syntax for the file format. We also recommend that a
file or class name and description of purpose be included on the
same "printed page" as the copyright notice for easier
identification within third-party archives.
Copyright [yyyy] [name of copyright owner]
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
Requirements and compatibility
Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta
“Works with” means the tool reads the open Agent Skills format; a skill written for one tool may use features others lack.
Needs: Needs Python
Security
What our scanner noticed· Low risk
- Scripts that your agent may run
This skill includes scripts that your agent may run. Read them before you use it.
A static scan is not a guarantee. Skills are third-party content: review a skill before you let an agent use it.
Attribution and licence
- Published by
- Google DeepMind
- Publisher
- Google DeepMind (Official)
- Source
- google-deepmind/science-skills · skills/chembl_database · commit 4de6786
- Licence
- Apache License 2.0 (redistribution allowed)
- LICENSE (added by AutoGineer from LICENSE)
- ATTRIBUTION.md (written by AutoGineer)
- Synced
AutoGineer is not affiliated with or endorsed by Google DeepMind.
Download ZIP
The ZIP holds the skill’s files, its licence files and an ATTRIBUTION.md. Download chembl-database.zip