KEGG

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a reference knowledge base for the systematic analysis of biological function from genome and molecular data. Initiated in 1995 and developed by the Kanehisa Laboratories in collaboration with Kyoto University's Bioinformatics Center, it integrates several interlinked databases — including PATHWAY (manually curated molecular network maps), GENES, KO (KEGG Orthology, the framework for functionally equivalent genes across organisms), COMPOUND and GLYCAN, REACTION, BRITE hierarchies, and the health-science DISEASE and DRUG collections. Rather than a single tool, KEGG is a resource accessed through a web interface and a public REST API.

From a graph-data perspective, KEGG's central artifact is the pathway map, a hand-drawn "molecular wiring diagram" whose machine-readable form is KGML (format:kgml-0.7.2), an XML exchange format. A KGML document models a pathway as a graph: entry elements are nodes typed as gene, ortholog (KO), compound, enzyme, reaction, map, group (complexes) or brite, each carrying a KEGG identifier and a graphics subelement with x/y coordinates, shape and colour. relation elements are edges — ECrel (successive enzymatic steps), PPrel (protein-protein), GErel (gene expression), PCrel and maplink — refined by subtypes such as activation, inhibition, phosphorylation and binding. reaction elements link compound nodes as substrates and products with reversible/irreversible direction. Because coordinates are embedded, KGML captures both topology and the reference layout.

The REST API (rest.kegg.jp) exposes operations — list, get, find, link, conv, ddi — returning tab-delimited text, flat-file records, KGML, JSON (BRITE), images, and RDF serialisations such as Turtle (format:turtle) and N-Triples (format:n-triples). This makes KEGG a common upstream source in format-conversion pipelines: KGML is routinely transformed to format:sif, format:graphml, format:gml, format:sbml-l3v2 or format:biopax-l3 by dedicated tools including tool:kegggraph, tool:keggtranslator, tool:keggconverter, tool:kgml2sif and the tool:biopython Bio.KEGG module.

Strengths are its breadth, manual curation and stable cross-referenced identifiers, which make pathways interoperable with tools like tool:cytoscape. Limitations are practical: KGML captures the drawn map, not always the full underlying biochemistry, so complex reaction stoichiometry and regulatory logic can be lost on conversion; group/compound handling varies between exporters; and KEGG's licensing is restrictive — API and bulk FTP access for many use cases require a paid subscription, unlike fully open resources.