WikiPathways

Summary

WikiPathways is an open, community-curated database of biological pathways stored in machine-readable formats for visualization, enrichment, and multi-omic integration. Its metabolite and lipid curation connects experimental identifiers to pathway nodes and supports analysis in tools such as PathVisio and Cytoscape [1–4].

Metabolite Support

The 2018 update reported 2,614 pathways across 25 species and 3,133 annotated unique human metabolite nodes, a 158% rise from 2013; the proportion of human metabolite nodes without an identifier fell from 5% to 1%. Metabolite identifiers were normalized through Wikidata, ChEBI, and HMDB, with new links including LIPID MAPS and CompTox [1].

Pathway curation also records reaction direction, involved enzymes, and distinct chemical forms rather than leaving metabolites as untyped text labels. This is necessary for mapping experimental measurements onto explicit biochemical entities [1].

Access and Reuse

WikiPathways distributes monthly quality-checked releases in GPML, GMT, RDF, and SVG and provides daily or alternative-format downloads. OpenAPI-documented services and language clients support programmatic access, and the pathway content uses a CC0 public-domain dedication to facilitate reuse in resources such as Wikidata [1].

Lipidomics Integration

Lipidomics pathways are available through a dedicated Lipids Portal and can be imported into PathVisio or Cytoscape. However, precise lipid integration remains constrained by unresolved isomers and by pathway databases that often represent complex lipids only at parent-class level [2,4].

The LIPID MAPS collaboration adds expert-verified lipid pathways and reactions to WikiPathways and exposes them in LMSD, linking structural records with biochemical transformations [3].

Citations

[1] Slenter et al. 2018. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Supports: Pathway and metabolite counts, identifier curation, reaction annotation, downloads, APIs, quality assurance, and licensing. Location: Abstract; Updates for Biologists and Chemists; Data Availability; Reusability; Conclusion.

[2] Kyle et al. 2021. Interpreting the lipidome: bioinformatic approaches to embrace the complexity. Supports: Lipidomics portal, PathVisio/Cytoscape use, and limitations of pathway mapping for structurally complex lipids. Location: Integrating Lipidomics Data with Pathway Models.

[3] Conroy et al. 2024. LIPID MAPS: update to databases and tools for the lipidomics community. Supports: LIPID MAPS–WikiPathways curation and LMSD reaction integration. Location: Updates to LMSD.

[4] Fedorova et al. 2023. Guiding the choice of informatics software and tools for lipidomics research applications. Supports: WikiPathways' role in pathway/network analysis and conversion to Cytoscape networks. Location: Data Integration Solutions.