KGML

KGML (KEGG Markup Language) is the XML exchange format for the manually drawn pathway maps of KEGG (the Kyoto Encyclopedia of Genes and Genomes), developed and maintained by the Kanehisa Laboratories in Japan. Version 0.7.2, released in August 2016, is the current revision and added "brite" as an entry type. Each KGML file computationally encodes one KEGG pathway map, capturing both its graph structure and the graphics needed to redraw the canonical hand-curated diagram, plus the orthologous gene assignments that link the map to the KEGG GENES database.

The document root is a single pathway element (with name, org, and number attributes, e.g. path:ko00010) that defines one graph. Its nodes are entry elements, typed as ortholog, enzyme, reaction, gene, group, compound, map, brite, or other; each entry carries an id, a KEGG-identifier name, an optional link back to the KEGG database, and a child graphics element giving x/y position, width/height, shape (rectangle, circle, roundrectangle, line), and fg/bg colors. Edges come in two flavors. relation elements connect two entries and are typed ECrel, PPrel, GErel, PCrel, or maplink, with subtype children encoding semantics such as activation, inhibition, phosphorylation, or binding. reaction elements model chemical transformations with substrate, product, and alt children and a reversible/irreversible type. This gives KGML a dual view: entry+relation describes protein/gene networks, while entry+reaction describes the compound/metabolic network.

In the graph-data and conversion landscape, KGML sits alongside other pathway and systems-biology XML formats such as format:sbml-l3v2, format:biopax-l3, format:gpml, and format:sbgn-ml-0.3, and is frequently transcoded between them. The tool:kegg REST API serves KGML for academic use; tool:keggtranslator converts pathways to SBML, BioPAX, GraphML, SIF, and images, tool:kegggraph and tool:pax2graphml load them into graph objects, tool:kgml2sif extracts a simple format:sif interaction list, and tool:keggconverter and tool:cy3sbml bridge to SBML. For visualization, KEGGscape imports KGML into tool:cytoscape.

Its strengths are a compact, purpose-built schema, faithful reproduction of KEGG's authoritative layouts, and easy programmatic access to well-curated biology. Its limitations are real: KGML is a lossy projection of the richer underlying KEGG data (much reaction stoichiometry and kinetics are absent), the schema is comparatively informal, group and map "shortcut" entries complicate naive graph parsing, and full/non-academic use is governed by KEGG licensing rather than an open standard.