skills.rest
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kegg-database

Query KEGG biological pathways, gene mappings, and ID conversions via REST API.

Updated Aug 23, 2026
Search Tags:#bioinformatics#pathway analysis#gene mapping#kegg#metabolic pathways#database api
One-click install
npx skills add https://github.com/Rowtion/Bioclaw --skill kegg-database-rowtion
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/Rowtion/Bioclaw/tree/main/scientific-skills/kegg-database
Command: npx skills add https://github.com/Rowtion/Bioclaw --skill kegg-database-rowtion

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides direct access to the KEGG database, enabling users to query biological pathways, gene-pathway mappings, metabolic networks, and drug interactions without needing to navigate the KEGG website or complex API documentation.

Core Features & Use Cases

  • Pathway Analysis: Retrieve detailed information about metabolic pathways, signaling pathways, and disease pathways.
  • Gene-Pathway Mapping: Find which pathways are associated with specific genes or sets of genes.
  • ID Conversion: Seamlessly convert between KEGG identifiers and those from external databases like UniProt and NCBI Gene.
  • Use Case: A researcher wants to understand the biological context of a list of differentially expressed genes. They can use this Skill to find all KEGG pathways associated with these genes, helping to identify enriched biological processes.

Quick Start

Use the kegg-database skill to find all human pathways associated with the gene TP53.

Frequently Asked Questions about kegg-database

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

FAQPage Schema
How do I find KEGG pathways associated with a specific gene?▼

To find KEGG pathways for a specific gene, you can use this Skill to query gene-pathway mappings via the KEGG REST API, retrieving all metabolic and signaling pathways linked to your target gene.

What is the best way to convert KEGG identifiers to NCBI Gene or UniProt IDs?▼

The best way to convert KEGG identifiers to external database IDs like NCBI Gene or UniProt is by using this Skill's ID conversion feature, which queries the KEGG API to seamlessly translate between different biological database formats.

Can I retrieve metabolic network and drug interaction data from the KEGG database using Python?▼

Yes, you can retrieve metabolic network and drug interaction data from the KEGG database using Python. This Skill provides direct REST API access to query compounds, drugs, and metabolic pathways within your bioinformatics workflows.

Does the KEGG API Skill support querying biological pathways for differentially expressed genes?▼

Yes, the KEGG API Skill supports querying biological pathways for differentially expressed genes. You can input your gene list to identify enriched biological processes and map them directly to disease or signaling pathways.

Do I need an API key to access the KEGG database for pathway analysis?▼

You do not need a specific API key to perform standard KEGG pathway analysis and gene mapping with this Skill, as it provides direct REST API access to query biological pathways, compounds, and metabolic networks.

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