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liongkj
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pubchem-api-guide

Query PubChem compound properties and bioassay data via the PUG REST API.

Updated Mar 20, 2026
Search Tags:#compounds#chemistry#pubchem#structures#pharmacology#bioassay
One-click install
npx skills add https://github.com/liongkj/zotero-library-bridge-skills --skill pubchem-api-guide
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-api-guide
Source: https://github.com/liongkj/zotero-library-bridge-skills/tree/main/skills/pubchem-api-guide
Command: npx skills add https://github.com/liongkj/zotero-library-bridge-skills --skill pubchem-api-guide

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill provides programmatic access to PubChem via the PUG REST API, enabling researchers and developers to fetch compound data, properties, and bioassay results without manual lookups.

Core Features & Use Cases

  • Retrieve compound properties by name, CID, InChI, or SMILES for quick data integration.
  • Perform similarity searches and access bioassay data to compare compounds and assess activity.
  • Automate data collection, formatting, and export for cheminformatics pipelines and research workflows.

Quick Start

Fetch caffeine's molecular weight and canonical SMILES from PubChem using the PUG REST API.

Frequently Asked Questions about pubchem-api-guide

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

FAQPage Schema
How do I query PubChem compound properties using SMILES or InChI?▼

You can query PubChem compound data via the PUG REST API using a chemical identifier like name, CID, InChI, or SMILES to fetch molecular properties, structures, and bioassay results in JSON, XML, or CSV formats.

Do I need an API key to retrieve PubChem bioassay results programmatically?▼

No API key is required to retrieve PubChem bioassay results. The PUG REST API provides public data access without authentication, letting you fetch compound activity and similarity search results directly.

What is the best way to automate cheminformatics data collection from PubChem?▼

The best way to automate cheminformatics data collection from PubChem is via the PUG REST API, which supports programmatic queries by compound identifiers and exports multiple formats like JSON, XML, and CSV for pipeline integration.

Can I perform similarity searches on PubChem compounds without manual lookups?▼

Yes, you can perform similarity searches via the PUG REST API to compare compounds and fetch bioassay data without manual lookups. It supports automated retrieval of structures and properties.

What output formats are supported when exporting PubChem compound structures?▼

When exporting PubChem compound structures, the PUG REST API supports JSON, XML, and CSV formats, allowing researchers to format and export data directly into cheminformatics pipelines and workflows.

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