[Feedback] Site Feedback: LycoCyc database file for genes/pathways and glucosinolate error

[feedback at gramene.org]

URL         : http://pathway.gramene.org/LYCO/substring-search?type=NIL

Subject     : Site Feedback: LycoCyc database file for genes/pathways and glucosinolate error

Name        : Ted Toal

Email       : twtoal at ucdavis.edu

Organization: Brady Lab, UC Davis

Comments    : 

I downloaded file lycocyc3.0.1.dump_pwfids.txt from your LycoCyc download link and used it to identify pathways associated with genes, and to test sets of genes for enrichment for pathways.  This identified pathway PWY-1187, "glucosinolate biosynthesis from homomethionine".  Since tomato doesn't have glucosinolates, this seems wrong.  I thought maybe the newer version 3.3 of LycoCyc might have this fixed, so I downloaded the database archive and unpacked it.  There is no file named lycocyc3.3.dump_pwfids.txt but within the 3.3 folder I did find file pathways.col that had a similar format.  However, this file also still contains PWY-1187 for glucosinolate biosynthesis.  But when I search online for this pathway, it doesn't find it.  Am I looking in the correct database file to find the version 3.3 pathways and genes?

http://www.warelab.org/bugs/view.php?id=5022