Reactome biopax export causes issue with gene set export

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The gene set output from Reactome pathways is sometimes wrong. Many
pathways of only 1-2 genes get converted to gene sets with 100s of genes.

The issue is that reactome has next-steps which reference other pathways.
We should not traverse these when creating gene sets.  It may make sense to
never traverse pathway steps and instead just collect genes from all
interactions in the pathway, though this will need to be checked to ensure
it covers all cases.

Original issue reported on code.google.com by gba...@gmail.com on 3 Dec 2009 at 9:38

[GoogleCodeExporter]

The contents of  the Molecules tab in pathways, contains data from pathways 
that share pathwaysteps.

Example:
Glucose 6-phosphate is isomerized to form fructose-6-phosphate in Reactome 
should only contain 3 
molecules and in pathwaycommons it contains over 500.
http://www.pathwaycommons.org/pc/record2.do?id=579730&userMsg=Global%20Filters%2
0Updated.
http://www.reactome.org/cgi-bin/eventbrowser?
DB=gk_current&FOCUS_SPECIES=Homo%20sapiens&ID=70112&

Original comment by Nad.An...@gmail.com on 13 Jan 2010 at 7:28

[GoogleCodeExporter]

After some digging into cPath code used to construct the internal_link table 
(which is used to create the 
internal_family table) which is used to display pathway membership info pages 
and export snapshot dumps, I 
believe it is prohibitive to re-factor cPath to properly import the Reactome 
files.  At least the following 
options are available:

 * preprocess Reactome files, specifically pathway-steps & rdf id's so that proper traversal of the pathways by 
cPath  is ensured.  This preprocessing can be run on other datasources where 
this issue can arise.
 * ask Reactome (and other datasources) to do the preprocessing themselves
 * instead of importing Reactome species files (like Home sapiens), import individual pathway files, like 
"Glucose 6-phosphate is isomerized to form fructose-6-phosphate" obtained from 
the web pages directly 
(this seemed to fix the problem)

Original comment by Benjamin.Gross@gmail.com on 13 Jan 2010 at 8:15

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Original comment by rod...@gmail.com on 4 Jan 2013 at 4:19

• Added labels: Product-cPath
• Removed labels: Project-cPath

[GoogleCodeExporter]

cPath1 (and old PC) was deprecated.

Original comment by rod...@gmail.com on 6 Jan 2014 at 8:04

• Changed state: WontFix