kegg-database

Name: kegg-database
Availability: InStock
Author: robinbarvaag

Query KEGG biological pathways and gene mappings via REST API.

Updated Jan 10, 2026

Search Tags:#bioinformatics #pathway analysis #gene mapping #rest api #kegg #biological data

Ready to run

npx skills add https://github.com/robinbarvaag/poynt --skill kegg-database-robinbarvaag

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/robinbarvaag/poynt/tree/main/.github/skills/kegg-database
Command: npx skills add https://github.com/robinbarvaag/poynt --skill kegg-database-robinbarvaag

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 via its REST API, enabling users to query biological pathways, genes, compounds, and more for academic research.

Core Features & Use Cases

Pathway Analysis: Retrieve and analyze metabolic, genetic, and cellular pathways.
ID Mapping: Convert between KEGG IDs and external database identifiers (e.g., UniProt, NCBI Gene).
Data Retrieval: Fetch gene sequences, compound structures, and drug interactions.
Use Case: A researcher needs to find all human genes associated with a specific metabolic pathway and then retrieve their corresponding UniProt IDs for further analysis.

Quick Start

Use the kegg-database skill to find all human pathways linked to the gene hsa:10458.

Frequently Asked Questions about kegg-database

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

FAQPage Schema

How do I query biological pathways and gene mapping using the KEGG REST API?▼

You can retrieve biological pathways and map genes through direct HTTP requests to the KEGG REST API. This workflow fetches pathway data, gene sequences, and compound structures for academic research without requiring external bioinformatics packages.

What is KEGG ID conversion and how does it work for biological data retrieval?▼

KEGG ID conversion is the process of mapping internal KEGG database identifiers to external database identifiers like UniProt or NCBI Gene. It works by querying the REST API to fetch corresponding cross-references for downstream biological data analysis.

Can I use Python to fetch drug interactions and compound structures from KEGG?▼

Yes, you can use Python to fetch drug interactions and compound structures from KEGG. The workflow supports direct HTTP and REST operations, allowing Python scripts to query the database and retrieve specific biological data programmatically.

Does this approach require any external bioinformatics dependencies for pathway analysis?▼

No, this approach does not require external bioinformatics dependencies for pathway analysis. It relies on direct REST API access to the KEGG database, allowing you to execute queries using standard Python HTTP operations without additional libraries.

What's the best way to find all human genes associated with a specific metabolic pathway?▼

The best way to find human genes associated with a metabolic pathway is to query the KEGG REST API using the specific human pathway identifier. This retrieves all linked genes, which can then be processed for ID conversion to external databases like UniProt.

Are there limitations when using direct REST API access for large-scale gene-pathway mapping?▼

Limitations of using direct REST API access for large-scale gene-pathway mapping include potential rate limits and the need to manually handle HTTP responses. Users must parse raw text data from KEGG and manage query batching within their Python workflows.