Downloads

Export the curated KE-WikiPathways, KE-GO, and KE-Reactome mapping database in bioinformatics-ready formats.

Cite this dataset: 10.5281/zenodo.21920660

WikiPathways

Gene-set files

2026-08-10

For enrichment, e.g. fgsea / clusterProfiler.

KE-WikiPathways GMT
All mappings High confidence
KE-Centric GMT
All mappings High confidence

Full database export

2026-08-10

Complete KE-WikiPathways mappings with full provenance.

RDF/Turtle CSV JSON

Gene Ontology

Gene-set files

2026-06-15

For enrichment, e.g. fgsea / clusterProfiler.

KE-GO GMT
All mappings High confidence
KE-Centric GMT
All mappings High confidence

Full database export

2026-06-15

Complete KE-GO mappings with full provenance.

RDF/Turtle CSV JSON

Reactome

Gene-set files

v97

For enrichment, e.g. fgsea / clusterProfiler.

KE-Reactome GMT
All mappings High confidence
KE-Centric GMT
All mappings High confidence

Full database export

v97

Complete KE-Reactome mappings with full provenance.

RDF/Turtle CSV JSON
Note: GMT files are generated on demand and cached. First download may take up to 60 seconds while WikiPathways gene lists are fetched. Subsequent downloads are immediate.
Data Sources: Gene lists sourced from WikiPathways SPARQL (https://sparql.wikipathways.org/sparql). GO gene annotations from go_bp_gene_annotations_propagated.json (pre-computed). Gene sets are propagated over the GO is_a/part_of closure, so a term carries the genes annotated to all of its descendants (the GO true-path rule). License: CC0.