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pubchem-database

Query PubChem data by name, CID, or SMILES using PubChemPy and PUG-REST.

21|1|Updated Mar 19, 2026
Search Tags:#bioactivity#cheminformatics#pubchem#pubchempy#structure-search#property-extraction
One-click install
npx skills add https://github.com/OwnLabAI/ownlab --skill pubchem-database-ownlabai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/pubchem-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill pubchem-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

PubChem is a foundational resource for chemical data; this Skill provides programmatic access to PubChem via PUG-REST and PubChemPy to streamline compound discovery, property retrieval, and bioactivity exploration.

Core Features & Use Cases

  • Retrieve molecular properties such as MolecularWeight, CanonicalSMILES, XLogP, and TPSA for compounds identified by name, CID, SMILES, or InChI.
  • Perform similarity and substructure searches to identify related compounds and motifs.
  • Access bioactivity data, assay summaries, and PUG-View annotations for deeper insights.
  • Support batch processing and scripting with dedicated utilities and references for common workflows.

Quick Start

Install the included scripts and run a simple query against PubChem to fetch a few properties.

Frequently Asked Questions about pubchem-database

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

FAQPage Schema
How do I retrieve molecular properties from PubChem using a SMILES string?▼

To retrieve molecular properties from PubChem, query the compound by SMILES string to fetch data like MolecularWeight, CanonicalSMILES, XLogP, and TPSA. The scripts handle PUG-REST requests automatically to return the specified chemical properties.

What is the best way to batch process PubChem identifier conversions?▼

Batch processing PubChem identifier conversions is handled via included Python scripts utilizing PubChemPy and PUG-REST. These scripts manage rate limiting and error handling to reliably convert multiple compound identifiers across different formats.

Can I perform substructure and similarity searches on PubChem programmatically?▼

Yes, you can perform substructure and similarity searches on PubChem programmatically. The scripts query PUG-REST to identify related compounds and structural motifs based on your input identifiers or structural strings.

Does this approach support retrieving bioactivity data and assay summaries?▼

Retrieving bioactivity data and assay summaries is supported through PUG-View annotations. You can access deeper chemical insights by querying PubChem programmatically to extract bioactivity information for specified compounds.

How do I handle rate limiting when querying PubChem PUG-REST in Python?▼

Rate limiting when querying PubChem PUG-REST is handled internally by the provided Python scripts. The implementation manages request throttling and error handling automatically to prevent API timeout failures during compound data retrieval.

What chemical identifiers can I use to search for compounds in PubChem?▼

You can search for PubChem compounds using chemical identifiers including compound name, CID, SMILES, or InChI. The scripts query these inputs against PUG-REST to extract corresponding molecular properties and structural data.

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