Which organisms are supported by the KEGG skill?

It supports all organisms available in the KEGG database, including humans (hsa), mice (mmu), fruit flies (dme), and various bacteria and fungi.

Does this skill support batch processing?

Most KEGG operations within this skill support up to 10 entries per request, though certain formats like JSON and images are limited to single-entry retrieval.

Can I retrieve molecular structures and pathway images?

Yes, the skill can download compound structures in MOL or KCF formats and retrieve pathway maps as PNG images or KGML/JSON files.

Is this skill free for commercial use?

No, the KEGG API is made available specifically for academic use. Non-academic or commercial use of KEGG requires a separate commercial license.

How do I convert NCBI Gene IDs to KEGG IDs?

The skill includes a dedicated 'kegg_conv' function that allows you to map identifiers between KEGG and external databases like NCBI, UniProt, and PubChem.

KEGG Database Connector

Name: KEGG Database Connector
Author: Sologa

bySologa

0•

Data Science & ML

Provides direct access to the KEGG REST API for biological pathway analysis, gene mapping, and metabolic research.

The KEGG Database skill enables Claude to interact directly with the Kyoto Encyclopedia of Genes and Genomes (KEGG) to streamline complex bioinformatics workflows. It facilitates comprehensive querying of biological pathways, genes, compounds, and enzymes across thousands of organisms using standardized REST API operations. Researchers can perform seamless ID conversions between KEGG and external databases like UniProt or NCBI, analyze drug-drug interactions, and retrieve molecular structures or high-resolution pathway maps. Designed specifically for academic research, this skill simplifies tasks such as pathway enrichment analysis, gene-to-pathway mapping, and cross-database biological data integration.

Key Features

01Pharmacological tools for drug-drug interaction (DDI) checking

02Built-in ID conversion for UniProt, NCBI Gene, PubChem, and ChEBI

03Retrieval of protein/nucleotide sequences and chemical structure files

040 GitHub stars

05Direct REST API access to KEGG's extensive biological and genomic databases

06Automated gene-to-pathway mapping and metabolic network analysis

Use Cases

01Integrating KEGG pathway data with external datasets using UniProt or NCBI identifiers

02Visualizing metabolic reactions and pathways involving specific chemical compounds or enzymes

03Mapping differentially expressed genes to biological pathways for enrichment analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline kegg-database

For use in Claude.ai and ChatGPT

Download Skill