GPML

GPML (Graphical Pathway Markup Language, originally the GenMAPP Pathway Markup Language) is an XML-based file format for encoding biological pathway diagrams together with their layout. It was introduced as the successor to GenMAPP's older MAPP format and is developed and maintained by the PathVisio project at the Maastricht Centre for Systems Biology and Bioinformatics, with contributors including Martijn van Iersel, Thomas Kelder, Martina Kutmon, Anders Riutta, Alexander Pico and Finterly Hu. GPML is the native storage format of the PathVisio pathway editor and the interchange format of the WikiPathways community pathway database.

A GPML document has a root Pathway element that carries metadata (name, organism, license) and holds a flat list of graphical objects. The central element is DataNode, which represents a biological entity such as a gene, protein, metabolite or complex and is annotated with an Xref (a database identifier and datasource, e.g. Ensembl or ChEBI) so that the diagram is machine-readable rather than purely pictorial. DataNodes can carry State elements (for modifications). Interaction and GraphicalLine elements describe edges as sequences of Points with an arrowhead type; endpoints attach to nodes or to Anchors placed along other lines, allowing interactions to connect to interactions. Additional objects include Group (complexes and pathways-within-pathways), Label, Shape and coordinate-based Graphics children giving absolute x/y positions, dimensions and colors. Literature references use an embedded BioPAX block. The schema is versioned; long-lived GPML2013a was succeeded by GPML2021, and the Java library libGPML reads, writes and converts between the two.

In the graph-data world GPML is essentially an attributed, laid-out directed graph specialized for pathway semantics, which makes it a natural conversion source and target. It interoperates with the wider systems-biology stack: it can be imported and exported alongside format:biopax-l3, format:sbml-l3v2 and format:sbgn-ml-0.3, converts to and from format:kgml-0.7.2 (KEGG) and format:celldesigner, and opens as a network in tool:cytoscape via a GPML plugin. The tool:sbfc (Systems Biology Format Converter) and tool:pax2graphml sit in this ecosystem, and pathways can be published through tool:ndex or analyzed with tool:networkx after conversion.

Its strengths are a human-curated visual layout tied to standard identifiers, an open schema, and an active editor and repository ecosystem. Limitations follow from its scope: it is a diagram-plus-annotation format rather than a quantitative model, so it lacks the kinetic rate laws of SBML; its layout-centric, WikiPathways-oriented design and evolving schema versions can complicate lossless round-tripping with more abstract graph or ontology formats.