Issues downloading all pathways

[Caleb Lindgren]

Hello,

I want to download all the pathway files for Homo sapiens. According to the WikiPathways statistics page, there are currently 1200 pathways for Homo sapiens. However, when I download the Homo sapiens zip file from the downloads page, it only contains information for 621 pathways. Am I missing something?

Thanks in advance,

Caleb

[Alex Pico]

Good question. Sorry for the confusion!

WikiPathways hosts around 600 Reactome pathways for human. So, the total count at WikiPathways.org is correct. Our monthly data release, however, excludes these since Reactome has its own distribution effort for third party analysis tools, etc. So, the downloaded zip is also correct, but is just a particular subset.  If you want to include the Reactome content, then you can use our R library: https://www.bioconductor.org/packages/release/bioc/html/rWikiPathways.html or our RDF via SPARQL: https://www.wikipathways.org/index.php/Portal:Semantic_Web. 

 - Alex

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[Caleb Lindgren]

Gotcha, that makes sense. Thanks for your help!