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bio-db-tools

Query public biology databases and APIs for protein, variant, and pathway data.

126|8|Updated Mar 10, 2026
Search Tags:#bioinformatics#pathway analysis#protein annotation#variant analysis#database query#molecular structure
One-click install
npx skills add https://github.com/DrugClaw/DrugClaw --skill bio-db-tools
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-db-tools
Source: https://github.com/DrugClaw/DrugClaw/tree/main/skills/science/bio-db-tools
Command: npx skills add https://github.com/DrugClaw/DrugClaw --skill bio-db-tools

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides a streamlined way to query and retrieve data from a comprehensive suite of public biology databases, eliminating the need for manual API calls or complex scripting for common bioinformatics lookups.

Core Features & Use Cases

  • Database Querying: Access data from UniProt, RCSB PDB, AlphaFold DB, ClinVar, dbSNP, gnomAD, Ensembl, GEO, InterPro, KEGG, OpenTargets, Reactome, and STRING.
  • Data Retrieval: Fetch protein annotations, molecular structures, variant information, gene expression datasets, pathway data, and protein-protein interaction networks.
  • Use Case: When asked to find the protein structure for EGFR, this Skill can query the RCSB PDB database and return relevant PDB IDs and links.

Quick Start

Use the bio-db-tools skill to look up protein annotations for the UniProt accession P04637.

Frequently Asked Questions about bio-db-tools

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

FAQPage Schema
How do I query protein annotations from UniProt for a specific accession number?▼

You can query protein annotations by providing a UniProt accession number like P04637 to retrieve associated data. The Skill queries public biology databases and APIs directly, returning protein annotations without requiring manual API calls.

Can I retrieve molecular structures and PDB IDs for proteins like EGFR?▼

Yes, you can retrieve molecular structures by querying the RCSB PDB database for proteins like EGFR. The Skill queries the database and returns relevant PDB IDs and links for the requested molecular structures.

What is the best way to fetch variant information from dbSNP and ClinVar?▼

The best way to fetch variant information is to use this Skill to query dbSNP, ClinVar, and gnomAD directly. It supports retrieval of variant information by automating the HTTP communication with these public biology databases.

Do I need Python and the requests library to query pathway data from KEGG and Reactome?▼

Yes, you need Python with the requests library installed to query pathway data from KEGG and Reactome. The Skill relies on the requests library to handle HTTP communication for querying these public biology databases.

How do I get protein-protein interaction networks from the STRING database?▼

You can get protein-protein interaction networks by querying the STRING database through this Skill. It supports retrieval of interaction network data alongside gene expression datasets from GEO and pathway data.

What public biology databases can I query for gene expression datasets and target associations?▼

You can query GEO for gene expression datasets and OpenTargets for target associations. The Skill also supports querying Ensembl, InterPro, AlphaFold DB, and dbSNP for comprehensive molecular and variant data retrieval.

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