kegg-database

Name: kegg-database
Availability: InStock
Author: OwnLab

Query KEGG REST API for pathway, gene, compound, and reaction data.

21|1|Updated Mar 19, 2026

Search Tags:#bioinformatics #conversion #rest-api #pathway #drug-interaction #kegg #gene-id

Ready to run

npx skills add https://github.com/OwnLabAI/ownlab --skill kegg-database-ownlabai

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/kegg-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill kegg-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

KEGG REST API access is provided to enable programmatic retrieval and integration of pathway, gene, compound, and reaction data for bioinformatics workflows.

Core Features & Use Cases

Efficiently fetch KEGG metadata, entries, and cross-references via REST endpoints.
Enable programmatic gene-pathway mapping, pathway retrieval, and ID conversions for integration into analysis pipelines.
Use cases include pathway exploration, data aggregation across organisms, and reproducible KEGG-based analyses.

Quick Start

Query KEGG data directly by calling the Python helper functions in scripts/kegg_api.py to perform common operations.

Frequently Asked Questions about kegg-database

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

FAQPage Schema

How do I retrieve KEGG pathway and gene data programmatically for bioinformatics workflows?▼

You can retrieve KEGG pathway and gene data by calling Python helper functions that wrap the KEGG REST API, enabling programmatic access for bioinformatics workflows. Functions like kegg_get and kegg_list fetch detailed entries and database listings directly.

Can I convert external database IDs to KEGG gene IDs in batch?▼

You can convert external database IDs to KEGG gene IDs using the kegg_conv function. The tool enforces a 10-entry batch limit per REST API request to ensure successful ID conversion without hitting server constraints.

What is the best way to find drug interactions in KEGG reference pathways?▼

The best way to find drug interactions in KEGG reference pathways is using the kegg_ddi function. It queries the KEGG drug interaction database via REST endpoints to retrieve targeted interaction entries for bioinformatics analysis.

Does this KEGG REST API integration handle HTTP errors and cross-links between compounds and reactions?▼

Yes, this KEGG REST API integration handles HTTP errors gracefully and supports cross-links between compounds, reactions, and pathways. The kegg_link function retrieves these cross-references to map data across organism-specific and reference databases.

Why does my KEGG API search return fewer entries than expected?▼

Your KEGG API search may return fewer entries than expected because the integration enforces a 10-entry batch limit per request. This constraint ensures stable REST API communication but requires pagination for larger dataset retrieval.

When do I need KEGG REST API access for pathway exploration instead of manual database searches?▼

You need KEGG REST API access for pathway exploration when building reproducible analysis pipelines, aggregating data across organisms, or mapping genes to pathways programmatically. Manual searches cannot scale for data integration workflows requiring automated retrieval.