pubchem-database
Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.
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Install
Works with every agent the skills CLI supports.
npx skills add https://github.com/google-deepmind/science-skills --skill pubchem-database- 01
Install
Run the command in your project. The CLI asks which agents to install for.
- 02
Describe the task
Ask your agent for something this skill covers. It loads pubchem-database automatically when relevant.
- 03
Review the result
The agent follows the SKILL.md steps, scripts and references bundled with the skill.
SKILL.md
The instructions your agent reads when the skill is triggered.
PubChem Database
Prerequisites
uv: Read theuvskill and follow its Setup instructions to ensureuvis installed and on PATH.- User Notification: If .licenses/pubchem_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://pubchem.ncbi.nlm.nih.gov/docs/citation-guidelines and https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest, then (2) create the file recording the notification text and timestamp.
Quick Start
PubChem queries are executed via a robust Python wrapper script to respect terms-of-service and handle complex JSON parsing. This script allows safe multi-agent use of APIs.
Example: Resolve a chemical name to its Compound ID (CID)
uv run scripts/pubchem_api.py resolve --name "aspirin" --output result.json
Core Rules
- Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.
- Read the generated JSON output file, and process it with jq or code.
- Verify Facts: ALWAYS verify information retrieved from memory with a database query if the user asks for a specific fact that can be checked in PubChem. Do not rely solely on internal knowledge.
- Notification: If this skill is used, ensure this is mentioned in the output.
Core Capabilities
1. Compound Resolution (Name or InChI to Identifiers) Convert chemical/trade names or InChI strings into PubChem CIDs, SMILES, and InChIKeys.
uv run scripts/pubchem_api.py resolve --name "ibuprofen" --output result.json
# OR
uv run scripts/pubchem_api.py resolve --inchi "InChI=1S/C3/c1-3-2/i1+1" --output result.json
2. Physical & Chemical Property Retrieval Fetch computed properties (e.g., MolecularWeight, XLogP, TPSA).
uv run scripts/pubchem_api.py properties --cid 2244 --output result.json
3. Synonyms and Trade Names Find alternative names and brand names.
uv run scripts/pubchem_api.py synonyms --cid 2244 --output result.json
Advanced Context
4. Safety and Hazard Information (GHS) Retrieve Global Harmonized System hazard statements and handling precautions (uses PUG-View).
uv run scripts/pubchem_api.py safety --cid 2244 --output result.json
5. Drug and Medication Information Fetch FDA pharmacology data, mechanism of action, and therapeutic uses (uses PUG-View).
uv run scripts/pubchem_api.py pharmacology --cid 2244 --output result.json
6. Custom Heading (PUG-View) Retrieve any specific heading from the PUG-View system (e.g., 'Geometry', 'Crystal Structures').
uv run scripts/pubchem_api.py view --cid 3939 --heading "Crystal Structures" --output result.json
7. Image Generation Retrieve 2D chemical structure images. The script returns a Markdown-formatted image link.
uv run scripts/pubchem_api.py image --cid 2244 --output result.json
Complex Search & Biology
8. Structure-Based Searching (Similarity & Substructure) Find molecules similar to a SMILES string or containing a specific substructure.
uv run scripts/pubchem_api.py similarity --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --output result.json
and
uv run scripts/pubchem_api.py substructure --smiles "C1=CC=CC=C1" --output result.json
9. BioAssay & Target Interactions Identify genes or proteins a chemical interacts with.
uv run scripts/pubchem_api.py assays --cid 2244 --output result.json
Advanced Usage & Workflows
10. Cross-references (Xrefs) Fetch identifiers cross-referenced with a CID (e.g., PatentID, PubMedID).
uv run scripts/pubchem_api.py xrefs --cid 2244 --type "PatentID" --output result.json
11. Property Range Search Find CIDs within a specific property range.
Supported features include: molecular_weight, heavy_atom_count, xlogp,
tpsa, h_bond_donor_count, h_bond_acceptor_count, rotatable_bond_count,
exact_mass, monoisotopic_mass, and complexity.
uv run scripts/pubchem_api.py range --feature molecular_weight --min 400.0 --max 400.05 --output result.json
12. Custom PUG-REST Query Execute a raw path against the PUG-REST API.
uv run scripts/pubchem_api.py query --path "compound/cid/2244/xrefs/PatentID/JSON" --output result.json
Fallback Search Strategies
If direct resolution by name or formula fails (e.g., for complex compounds or specific ions):
- Search for parent/neutral molecule: If searching for an ion or salt, try searching for the neutral parent compound.
- Deconstruct complex formulas: If a complex formula returns no results, try searching for major components or ligands.
- Use substructure or similarity search: If you have a SMILES string or can generate one for a component, use it to find related compounds.
Complex Queries and Multi-Step Tasks
- Custom/Complex Queries: For more details, read references/endpoints.md to construct raw PUG-REST URLs.
- Multi-Step Tasks: For complex tasks like drug discovery pipelines, follow the checklists in references/workflows.md.
FAQ
What does the pubchem-database skill do?
Query PubChem, search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics. Use when a user asks about a specific chemical, drug, or molecule.
How do I install pubchem-database?
Run npx skills add https://github.com/google-deepmind/science-skills --skill pubchem-database in your project. The skills CLI detects the agents you use and copies the skill into the right folder. For Claude Code you can also place the skill folder at ~/.claude/skills/pubchem-database/ (personal) or .claude/skills/pubchem-database/ (project).
Which AI agents can use pubchem-database?
Any agent that supports the open Agent Skills format (a folder with a SKILL.md file), including Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, Windsurf, Cline, OpenCode and more.
Is pubchem-database safe to install?
No partner security audit is available yet. Skills can run commands and scripts, so read the SKILL.md and any bundled files before installing.
Who maintains pubchem-database?
It is published by google-deepmind in google-deepmind/science-skills. It has 2,233 recorded installs.
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