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kegg-database

Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.

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@K-Dense-AI

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KEGG Database - Biological Pathway Analysis REST API Tool

Skill Overview


The KEGG Database skill provides a Python interface for direct access to the KEGG (Kyoto Encyclopedia of Genes and Genomes) REST API, for biological pathway analysis, gene-to-pathway mapping, metabolic network research, and drug interaction analysis.

Applicable Scenarios

  • Biological informatics research

    • Query and analyze biological pathway data to obtain relationship networks of genes, compounds, enzymes, diseases, and drugs; supports pathway enrichment analysis and metabolic network construction.

  • Genomics and transcriptomics analysis

    • Map gene lists to KEGG pathways, identify biological processes involving genes, and support cross-species pathway comparison and gene function annotation.

  • Drug discovery and chemoinformatics

    • Query drug–drug interactions, analyze compound involvement in metabolic reactions, and study drug target pathways and disease association mechanisms.

    Core Features

  • Seven KEGG API operations

    • Supports database information queries (kegg_info), entry listing (kegg_list), keyword searching (kegg_find), entry retrieval (kegg_get), ID conversion (kegg_conv), cross-references (kegg_link), and drug–drug interaction checks (kegg_ddi), covering all of KEGG's REST API functionality.

  • Multiple output formats

    • Supports retrieval of protein/nucleotide sequences (FASTA), compound structures (MOL/KCF), pathway images (PNG), pathway maps (KGML/XML), pathway data (JSON), and other formats to meet different analysis needs.

  • Cross-database ID mapping

    • Supports ID conversion with external databases such as NCBI Gene, UniProt, PubChem, ChEBI, etc., facilitating integration of multi-source biological data for joint analysis.

    Frequently Asked Questions

    Is the KEGG API free to use?


    The KEGG API is free only for academic users and academic purposes. If you belong to a non-academic institution or plan to use the data for commercial purposes, you must obtain a commercial license from KEGG.

    What is the maximum number of records per query?


    Except that images, KGML, and JSON formats only support single records, most KEGG API operations (such as kegg_get, kegg_list, kegg_conv) support batch queries of up to 10 entries per request.

    Should I use the direct KEGG API or bioservices?


    If your project only needs access to the KEGG database, use this skill's direct HTTP/REST interface. If you need to integrate multiple biological databases (e.g., UniProt, PubChem, ChEMBL), it is recommended to use the bioservices package for a more unified interface.