Homo Sapiens count of pathways discrepancy

[jomo018]

Hello, 

I am using R command: 

downloadPathwayArchive(date="current", organism="Homo Sapiens", format="gmt")

and obtain 556 pathways. 

However

listPathwayIds('Homo sapiens')

shows 1136 pathways. 

Any ideas what I am doing wrong?

Jonathan 

[Alex Pico]

You are doing it right. There are many ways to count pathways…. The monthly release via downloadPathwayArchive is the set of pathways that have been approved for use for pathway analysis, etc. This is the set that gets distributed to tools like Enrichr, WebGestalt and clusterProfiler.  Via web services (and the rWikiPathways) you can also access the content that pending review, under construction, etc. These other categories are useful for other, non-analysis use cases like identifying pathways to curate, etc. It also includes all the Reactome pathways, which we keep separate from our other content for analysis purposes (via the monthly releases), but is technically part of the WikiPathways content and amenable to curation and analysis just like any other pathway at WikiPathways.

Hope that helps,

 - Alex

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