Can I retrieve protein or nucleotide sequences?

Yes, the skill can fetch sequences in FASTA format using the 'aaseq' (amino acid) or 'ntseq' (nucleotide) parameters.

Is the KEGG Database skill free for commercial use?

No, the KEGG REST API is provided for academic use only. Commercial organizations require a license from Pathway Solutions for use.

What organisms are supported by this skill?

The skill supports thousands of organisms included in the KEGG genome database, using standard codes like 'hsa' for humans, 'mmu' for mice, and 'eco' for E. coli.

How do I convert external IDs to KEGG IDs?

You can use the built-in kegg_conv function to map identifiers between KEGG and databases like UniProt, NCBI-GeneID, or PubChem.

KEGG Database Pathway Analysis

Name: KEGG Database Pathway Analysis
Author: lifangda

bylifangda

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データサイエンスとML

Accesses the KEGG REST API to perform biological pathway analysis, gene-pathway mapping, and metabolic network research.

概要

This skill provides direct access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) for advanced bioinformatics workflows. It enables researchers to query complex biological data including pathways, genes, enzymes, and drug interactions across thousands of organisms. Designed for academic use, the skill streamlines tasks such as ID conversion between KEGG and external databases (NCBI, UniProt, PubChem), pathway enrichment analysis, and the retrieval of molecular structures or sequences, allowing for seamless integration of biological intelligence into automated Python workflows.

主な機能

Cross-database ID conversion for NCBI GeneID, UniProt, and PubChem
Keyword searching for genes, compounds, and drugs by formula or mass
16 GitHub stars
Direct REST API access to KEGG databases including Pathway, Brite, and Genes
High-resolution pathway image retrieval and KGML/JSON data extraction
Drug-drug interaction (DDI) checking and pharmacological network analysis

ユースケース

Integrating genomic data from external databases with KEGG functional annotations
Mapping experimental gene lists to biological pathways for enrichment analysis
Analyzing metabolic networks and compound-reaction relationships for drug discovery

概要

主な機能

Cross-database ID conversion for NCBI GeneID, UniProt, and PubChem
Keyword searching for genes, compounds, and drugs by formula or mass
16 GitHub stars
Direct REST API access to KEGG databases including Pathway, Brite, and Genes
High-resolution pathway image retrieval and KGML/JSON data extraction
Drug-drug interaction (DDI) checking and pharmacological network analysis

ユースケース

Integrating genomic data from external databases with KEGG functional annotations
Mapping experimental gene lists to biological pathways for enrichment analysis
Analyzing metabolic networks and compound-reaction relationships for drug discovery