kegg-database

Retrieve KEGG pathways, genes, compounds, and drugs via REST operations.

21|2|Updated Dec 8, 2025

Search Tags:#bioinformatics #pathway analysis #drug interactions #rest api #kegg #id conversion

Ready to run

npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill kegg-database-silverstein

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: kegg-database
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/kegg-database
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill kegg-database-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

KEGG pathway and molecular interaction lookups are slow and fragmented when you need consistent REST access across genes, pathways, compounds, and drugs.

Core Features & Use Cases

Direct KEGG REST API Operations: Retrieve pathway/map details, gene and compound entries, and drug information with consistent endpoints.
Automated Python Helper Functions: Use dedicated functions to perform listing, keyword/molecular searching, entry retrieval, ID conversion, cross-referencing, and drug-drug interaction checks.
Academic-Use Controlled Access: Supports academic workflows that require KEGG-specific control and clear operation constraints.
Reference-Driven Guidance: Pair operational helpers with comprehensive API documentation for formats, organism codes, limits, and best practices.

Quick Start

Use the kegg-database skill to retrieve the glycolysis pathway entry for humans by running a single KEGG GET request for hsa00010.

Frequently Asked Questions about kegg-database

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

FAQPage Schema

How do I query KEGG pathways and retrieve gene entries using a REST API?▼

Query KEGG pathways and retrieve gene entries by executing formatted REST-style GET, list, and find requests directly against the https://rest.kegg.jp endpoint. This approach provides consistent access to pathway maps, gene details, and molecular interaction data for academic workflows.

What is the best way to convert biological IDs across different KEGG resources?▼

Convert biological IDs across KEGG resources by utilizing dedicated conv operations to map genes, compounds, and pathways. This cross-referencing method ensures accurate ID conversion between distinct biological databases for academic pathway analysis.

Can I check drug-drug interactions in KEGG for academic research?▼

Check drug-drug interactions in KEGG by sending formatted ddi requests to the REST API. This retrieves specific drug interaction data, supporting academic research workflows that require controlled access to molecular interaction networks.

Does the KEGG REST API require network access for pathway analysis?▼

Yes, KEGG REST API pathway analysis requires active network access to https://rest.kegg.jp. The retrieval operations for genes, compounds, and drugs depend on external connectivity to fetch formatted query results.

How do I map specific genes to metabolic pathways in KEGG?▼

Map genes to metabolic pathways by using link operations to cross-reference gene entries with pathway maps. This identifies functional connections within metabolic pathway exploration and yields structured biological relationship outputs.

Are there documented limits for KEGG API requests when retrieving compound entries?▼

Yes, retrieving compound entries and other KEGG API requests operate under documented limits and specific output formats. The reference-driven guidance details these constraints to ensure queries remain within acceptable operational boundaries.