tooluniverse-chemical-compound-retrieval

Retrieve and validate chemical compound data from PubChem and ChEMBL APIs.

1.6k|244|Updated Mar 3, 2025

Search Tags:#bioactivity #ChEMBL #PubChem #compound #data-retrieval #identifiers #drug-information

Ready to run

npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-chemical-compound-retrieval

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: tooluniverse-chemical-compound-retrieval
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/skills/tooluniverse-chemical-compound-retrieval
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-chemical-compound-retrieval

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill provides a unified workflow to retrieve and validate chemical compound data from PubChem and ChEMBL, creating reliable profiles with identifiers, properties, bioactivity, and drug information.

Core Features & Use Cases

Disambiguation and cross-database validation of compound identity (PubChem CID, ChEMBL ID, SMILES, InChI)
Comprehensive compound profiling: identifiers, molecular properties, bioactivity data, and potential drug information
Use cases include drug candidate verification, SAR analysis, and research data curation

Quick Start

Use the tooluniverse chemical compound retrieval skill to obtain a complete compound profile for a given query (name, CID, or SMILES). For example, retrieve the PubChem CID and ChEMBL cross-reference for a known drug and fetch its molecular weight and LogP.

Frequently Asked Questions about tooluniverse-chemical-compound-retrieval

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

FAQPage Schema

How do I retrieve and consolidate chemical compound data from PubChem and ChEMBL?▼

To retrieve chemical compound data, provide a query like a compound name, PubChem CID, or SMILES. The skill extracts and consolidates validated identifiers, properties, and bioactivity information from both PubChem and ChEMBL APIs into a unified profile.

How do I validate a compound identity across PubChem and ChEMBL?▼

Validating a compound identity across PubChem and ChEMBL requires cross-database confirmation using standard identifiers like PubChem CID, ChEMBL ID, SMILES, or InChI. The skill disambiguates ambiguous queries to ensure accurate chemical matching.

What is the best way to build a complete chemical compound profile for drug candidate verification?▼

The best way to build a chemical compound profile for drug candidate verification is extracting molecular properties, bioactivity data, and drug labels from PubChem and ChEMBL. This consolidates validated identifiers and bioactivity metrics into a single reliable output.

Can I use a SMILES string to fetch bioactivity data from ChEMBL and PubChem?▼

Yes, you can use a SMILES string to fetch bioactivity data from ChEMBL and PubChem. The skill uses standard HTTP requests to process SMILES queries, disambiguate the compound, and retrieve available bioactivity and drug information.

Does this chemical data retrieval process work with ambiguous compound names?▼

Yes, the chemical data retrieval process works with ambiguous compound names. It features built-in disambiguation and cross-database identity confirmation to accurately resolve ambiguous queries and retrieve the correct molecular properties and bioactivity data.