Which organisms are supported for pathway analysis?

The skill supports all KEGG-indexed organisms, including common codes like hsa (human), mmu (mouse), dme (fruit fly), and eco (E. coli).

Is the KEGG Database skill free for commercial use?

No, access to the KEGG API via this skill is strictly for academic use. Commercial entities must obtain a license from KEGG before using their data or API services.

Can I retrieve gene sequences using this skill?

Yes, the skill supports retrieving both protein (aaseq) and nucleotide (ntseq) sequences in FASTA format for specified gene entries.

Does this skill support identifier mapping?

Yes, it provides robust ID conversion capabilities between KEGG IDs and external databases like NCBI-GeneID, UniProt, PubChem, and ChEBI.

KEGG Database Explorer

Name: KEGG Database Explorer
Author: jimmc414

byjimmc414

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324

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Data Science & ML

Accesses the KEGG REST API to perform biological pathway analysis, gene mapping, and molecular interaction research.

The KEGG Database skill empowers Claude to interact directly with the Kyoto Encyclopedia of Genes and Genomes, a vital resource for bioinformatics and systems biology. It enables complex scientific operations such as querying metabolic pathways, mapping genes to biological functions, and investigating drug-drug interactions. By providing specialized Python helper functions for ID conversion, pathway enrichment, and molecular search, this skill bridges the gap between raw biological data and autonomous scientific discovery, making it an essential tool for researchers using Claude Code in academic environments.

Key Features

01Identifier conversion between KEGG, UniProt, NCBI Gene, and PubChem

02Automated workflows for pathway enrichment and cross-organism analysis

03Advanced chemical search by formula, exact mass, and molecular weight

04Multi-format data retrieval including FASTA, MOL, PNG, and KGML

05Direct REST API access to KEGG pathways, genes, compounds, and enzymes

06324 GitHub stars

Use Cases

01Investigating drug-drug interactions and pharmacological molecular networks

02Comparing pathway conservation across different organisms using genome-specific identifiers

03Mapping lists of genes to metabolic or signaling pathways for enrichment analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos kegg-database

For use in Claude.ai and ChatGPT