pubchem-database - SKILL.md Agent Skill

name: pubchem-database description: > 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.

PubChem Database

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill 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.