skills.rest
BKZhao
BKZhaoCOMMUNITY
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kegg-database

Retrieve KEGG data and convert identifiers via the REST API.

Updated Aug 23, 2026
Search Tags:#rest#bioinformatics#data-retrieval#gene#pathway#kegg
One-click install
npx skills add https://github.com/BKZhao/MIMIC-Papers-Repro-Agent --skill kegg-database-bkzhao
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/BKZhao/MIMIC-Papers-Repro-Agent/tree/main/.codex/skills/kegg-database
Command: npx skills add https://github.com/BKZhao/MIMIC-Papers-Repro-Agent --skill kegg-database-bkzhao

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

KEGG REST data access often requires manual, fragmented querying across multiple databases. This Skill centralizes programmatic access to KEGG's REST API to streamline cross-database lookups, cross-references, and data retrieval for integration into analytics pipelines.

Core Features & Use Cases

  • Database discovery and metadata: fetch KEGG database info and organism data.
  • Listing and searching: list entries and search by keywords, formulas, or IDs.
  • Data retrieval and conversion: fetch entries in various formats (KGML, aaseq, ntseq, json) and convert IDs across external databases.
  • Use Case: Build a pipeline to pull human pathway data and associated gene lists for enrichment analysis and downstream visualization.
  • Use this for direct HTTP/REST work or KEGG-specific control.

Quick Start

Query the hsa00010 glycolysis pathway and fetch its KGML data for downstream analysis.

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 data and gene lists programmatically for enrichment analysis?▼

To retrieve KEGG pathway data programmatically, you can query specific databases, list entries, and fetch data in formats like KGML, aaseq, ntseq, or JSON. This centralizes cross-database lookups and data retrieval for integration into analytics pipelines.

Can I convert external database identifiers to KEGG IDs using the REST API?▼

Yes, you can convert IDs across external databases using the KEGG REST API. The Skill performs identifier conversions to support cross-database mappings within reproducible bioinformatics workflows.

What formats can I fetch KEGG entries in when querying pathways and genes?▼

When querying KEGG entries for pathways and genes, you can fetch data in multiple formats including KGML, aaseq, ntseq, and JSON. This allows flexible data retrieval for downstream analysis and visualization.

Does the KEGG REST API have access restrictions for bioinformatics data retrieval?▼

Yes, KEGG REST API access enforces academic-use constraints and safe usage patterns. The Skill ensures data retrieval and identifier conversions respect KEGG's access restrictions when integrated into data pipelines.

How do I search KEGG database entries by keywords or molecular formulas?▼

You can search KEGG database entries by keywords, formulas, or IDs through the REST API. This enables targeted entry listing and discovery for bioinformatics workflows requiring specific pathway or gene data.

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