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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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Pathway Missing to from pathways.txt #258

Closed cannin closed 7 years ago

cannin commented 8 years ago

This exists in Pathway Commons 8: http://www.pathwaycommons.org/pc2/get?uri=http://identifiers.org/reactome/R-HSA-1640170

This does not exist in the pathways.txt from http://www.pathwaycommons.org/archives/PC2/current/pathways.txt.gz: grep "http://identifiers.org/reactome/R-HSA-1640170" pathways.txt

http://identifiers.org/reactome/R-HSA-1640170 is Reactome Cell Cycle

IgorRodchenkov commented 8 years ago

Confirmed. It's a root/top pathway.

Now looking...

IgorRodchenkov commented 8 years ago

Sadly, indeed, there seems to be a bug in how the pathways.txt (pathways hierarchy) was generated.

Here is another example of missing pathway R-HSA-73894 from Reactome: "http://identifiers.org/reactome/R-HSA-73894" ("DNA Repair", large pathway)

However, other "top pathways" (from Reactome) are present there in the pathways.txt, e.g. "http://identifiers.org/reactome/R-HSA-76044" (a smaller one), "http://identifiers.org/reactome/R-HSA-382551" (as large as missing R-HSA-73894 one) or "http://identifiers.org/reactome/R-HSA-74160" (much larger pathway)...

I am still looking... (looks, pathway size or being root/top does not help me to know why some were excluded from the file...)

IgorRodchenkov commented 7 years ago

Fixed Paxtools bug BioPAX/Paxtools#20, generated a new pathways.txt file and replaced it and paxtools.jar in http://www.pathwaycommons.org/archives/PC2/current/