From the Supplementary material in their paper:
"ClueGO allows also KEGG updates via SOAP API. ClueGO KEGG based files will have in the name the date of the download. The KEGG update rate: http://www.genome.jp/en/info dbget.html. Since Biocarta is not frequently changing and only supports human and mouse, updates will be supplied with each new release of ClueGO. BioCarta source files are taken from REACTOME via SOAP API. Source files and interfaces used: 1. GO Ontology, in OBO format: ftp://ftp.geneontology.org/pub/go/ontology/gene ontology edit.obo 2. GO Annotation files: ftp://ftp.geneontology.org/pub/go/gene-associations/ 3. KEGG API: http://www.genome.jp/kegg/soap/ 4. Biocarta API: http://www.reactome.org/download/index.html"