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PathwayCommons / cpath2

Biological pathway data integration and access platform (Pathway Commons)
http://www.pathwaycommons.org/pc2/
MIT License
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An example query returns "no results" after adding format=gsea despite there are proteins in the sub-model #191

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
It's probably a bug in the GSEA converter (Paxtools, gsea-converter). Because, 
with IL1B, there are two Pathways in the sub-model (but pathways are weird, 
contain no components, which is not unusual in PID data); whereas, without 
IL1B, the OWL has no pathways at all, and GSEA converter uses all PRs.

Example.

http://www.pathwaycommons.org/pc2/graph?kind=neighborhood&datasource=pid&source=
BCL10&source=FOSL1&source=IL1A&source=IL1B

- gets an owl, but when I add the format=gsea at the end -

http://www.pathwaycommons.org/pc2/graph?kind=neighborhood&datasource=pid&source=
BCL10&source=FOSL1&source=IL1A&source=IL1B&format=gsea

It says no results found. But strangely if I remove IL1B from the source, it 
works:

http://www.pathwaycommons.org/pc2/graph?kind=neighborhood&datasource=pid&source=
BCL10&source=FOSL1&source=IL1A&format=gsea

Original issue reported on code.google.com by rod...@gmail.com on 13 Nov 2014 at 8:02

GoogleCodeExporter commented 9 years ago 
Fixed in Paxtools 4.3.1-SNAPSHOT sources and PC2 v6.
Try 
http://webservice.baderlab.org:48080/graph?kind=neighborhood&datasource=pid&sour
ce=BCL10&source=FOSL1&source=IL1A&source=IL1B&format=gsea

Original comment by rod...@gmail.com on 18 Nov 2014 at 11:20