Pubchem 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 PubChem Database skill provides a structured interface to interact with the PubChem API. It enables users to perform chemical informatics tasks such as resolving chemical names to identifiers, retrieving physical and chemical properties, performing similarity or substructure searches, and accessing pharmacology or safety data. The skill utilizes a dedicated Python wrapper script to ensure API rate limits are respected and data is parsed consistently.
What it does
- Resolves chemical names, InChI, or SMILES strings into PubChem CIDs.
- Retrieves physical and chemical properties like molecular weight and XLogP.
- Performs similarity and substructure searches to identify related compounds.
- Fetches GHS safety, hazard information, and FDA pharmacology data.
- Generates 2D chemical structure images.
- Identifies gene or protein interactions via bioassay data.
When to use it
- When you need to verify chemical facts or properties for a specific molecule.
- When performing cheminformatics research or drug discovery workflows.
- When identifying safety precautions or pharmacological data for a chemical substance.
- When searching for compounds similar to a specific chemical structure.
Advantages
- Enforces API rate limits automatically via the provided wrapper.
- Provides structured JSON output for reliable data processing.
- Supports complex workflows like comprehensive chemical profiling and bioassay lookups.
- Ensures consistent handling of chemical identifiers and search parameters.
Usage examples
- “What is the molecular weight and XLogP of aspirin?”
- The agent resolves 'aspirin' to its CID, then queries the properties endpoint to return the requested chemical data.
- “Find compounds similar to this SMILES string: CC(=O)OC1=CC=CC=C1C(=O)O”
- The agent performs a 2D similarity search against the PubChem database and returns a list of related chemical identifiers.
- “What are the safety hazards for ibuprofen?”
- The agent retrieves the GHS hazard statements and handling precautions for ibuprofen using the PUG-View system.
- “Show me the 2D structure of caffeine.”
- The agent resolves caffeine to its CID and retrieves a Markdown-formatted link to its 2D chemical structure image.
Install
Download the skill as a ZIP:
https://autogineer.com/agent-skills/google-deepmind/pubchem-database/downloadUnzip it into the cross-client skills folder of your project:
mkdir -p .agents/skills && unzip pubchem-database.zip -d .agents/skills
Documentation by Google DeepMind
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.jsonCore 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.json2. Physical & Chemical Property Retrieval Fetch computed properties (e.g., MolecularWeight, XLogP, TPSA).
uv run scripts/pubchem_api.py properties --cid 2244 --output result.json3. Synonyms and Trade Names Find alternative names and brand names.
uv run scripts/pubchem_api.py synonyms --cid 2244 --output result.jsonAdvanced 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.json5. 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.json6. 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.json7. 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.jsonComplex 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.jsonand
uv run scripts/pubchem_api.py substructure --smiles "C1=CC=CC=C1" --output result.json9. BioAssay & Target Interactions Identify genes or proteins a chemical interacts with.
uv run scripts/pubchem_api.py assays --cid 2244 --output result.jsonAdvanced 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.json11. 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.json12. 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.jsonFallback 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.
Files
- ATTRIBUTION.mdAdded by AutoGineer914 B
- LICENSELicence file added by AutoGineer11.1 KiB
- SKILL.md5.5 KiB
- references/citation.bib2.0 KiB
- references/endpoints.md2.4 KiB
- references/workflows.md1.4 KiB
- scripts/pubchem_api.pyScript11.3 KiB
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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
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Attribution and licence
- Published by
- Google DeepMind
- Publisher
- Google DeepMind (Official)
- Source
- google-deepmind/science-skills · skills/pubchem_database · commit 4de6786
- Licence
- Apache License 2.0 (redistribution allowed)
- LICENSE (added by AutoGineer from LICENSE)
- ATTRIBUTION.md (written by AutoGineer)
- Synced
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