skills.rest
google-deepmind
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pubchem-database

Resolve chemical names, InChI, or SMILES into PubChem CIDs and retrieve identifiers, properties, safety text, and pharmacology annotations.

2.7k|283|Updated May 13, 2026
Search Tags:#cheminformatics#pubchem#pharmacology#structure search#compound resolution#safety data#assay lookup
One-click install
npx skills add https://github.com/google-deepmind/science-skills --skill pubchem-database-google-deepmind
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/pubchem_database
Command: npx skills add https://github.com/google-deepmind/science-skills --skill pubchem-database-google-deepmind

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires scienceskillscommon, and includes scripts (resource) and references (resource) components.

What problem does it solve?

It helps you reliably look up chemical and drug information—like identifiers, properties, safety, and pharmacology—without guessing or relying on outdated memory.

Core Features & Use Cases

  • Resolve chemicals to identifiers: Convert a name or InChI into PubChem CIDs plus canonical identifiers like SMILES and InChIKey.
  • Fetch structured chemical properties: Retrieve computed descriptors (e.g., molecular weight, logP, TPSA) for analysis and comparison.
  • Search by structure and bioactivity: Run similarity or substructure searches and then pull assay summaries and cross-references for research.
  • Use PubChem annotations safely: Obtain text sections (e.g., GHS safety, pharmacology) via PUG-View and include the required notification in output.

Quick Start

Use the pubchem-database skill to resolve "aspirin" into its CID and SMILES, using the wrapper script output for downstream analysis.

Frequently Asked Questions about pubchem-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I resolve a chemical name or SMILES into a PubChem CID and canonical identifiers?▼

Resolve chemical names, InChI, or SMILES into PubChem CIDs using the pubchem_api.py wrapper, which calls PUG-REST endpoints and returns canonical SMILES and InChIKey outputs for downstream analysis.

Can I retrieve computed molecular properties like logP and TPSA from PubChem?▼

Retrieve computed chemical descriptors such as molecular weight, logP, and TPSA from PubChem by querying structured properties through the PUG-REST API wrapper, outputting results to JSON for compound profiling.

How do I run substructure and similarity searches to find bioactivity assay data?▼

Run similarity or substructure searches via PUG-REST to find matching CIDs, then pull assay summaries and cross-references including patents and PubMed IDs for target exploration and pharmacology research.

How do I fetch GHS safety data and pharmacology text without hitting API rate limits?▼

Fetch GHS safety text and pharmacology annotations via PUG-View endpoints using the wrapper's enforced rate-limited API access, ensuring PubChem annotations include the required notification in JSON output.

Do I need the scienceskillscommon dependency to query PubChem compound data?▼

The scienceskillscommon dependency is required to provide the foundational environment and shared utilities needed before the pubchem-database scripts can execute PUG-REST and PUG-View API calls effectively.

What's the best way to cross-reference PubChem compounds with patents and PubMed IDs?▼

Cross-reference PubChem compounds with patents and PubMed IDs by resolving compound names to CIDs, then retrieving structured cross-references through the PUG-REST wrapper to generate linked JSON outputs for cheminformatics workflows.

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