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Revision 1.2 - (download) (as text) (annotate)
Wed Dec 7 19:38:22 2005 UTC (13 years, 10 months ago) by golsen
Branch: MAIN
CVS Tags: rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, rast_rel_2008_09_30, caBIG-13Feb06-00, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, caBIG-05Apr06-00, rast_rel_2009_0925, rast_rel_2010_1206, rast_rel_2010_0118, rast_rel_2009_02_05, rast_rel_2011_0119, rast_rel_2008_12_18, rast_rel_2008_10_09, rast_release_2008_09_29, rast_rel_2008_04_23, rast_rel_2008_08_07, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, rast_rel_2008_10_29, rast_rel_2009_03_26, rast_rel_2008_11_24, HEAD
Changes since 1.1: +1 -1 lines
Don't mean to be pedantic, but I figured that I might as well add newlines
at the end of text files that lack one.  Identified with a script:

/bin/sh -O extglob -c 'for f in */*.@(c|css|html|js|pl|pm|py|TXT); do perl -e '"'"'while(<>) {$s = ! /\n$/} exit $s'"'"' $f || echo $f; done'

fixed with a script:

for file in _list_; do echo "" >> $file; done

<h1>Integration of KEGG pathways and Subsystems in the SEED</h1>
Kevin Formsma (Kevin.Formsma@hope.edu)<br>
Matt DeJongh (dejongh@hope.edu)<br>
This enhancement to the subsystem page enables users to locate functional roles in KEGG maps
by matching EC numbers specified in the functional roles.  It also uses the XML format of the KEGG maps (called KGML) to search for EC numbers in the vicinity of the subsystem's functional roles that should perhaps be added to the subsystem.
To perform the analysis, navigate in your browser on your SEED server
to /FIG/subsys_hope.cgi.  Choose your subsystem to view as normal.  To
run the analysis for that subsystem, check the box 'show KEGG data'
and click on 'show spreadsheet'.  This will refresh the current page.
Scroll down to the bottom where you will see names of KEGG pathways
containing the functional roles in the subsystem (if any).  Beside
each pathway there are two links: the first displays the pathway
highlighting EC's already in the subsystem, and the second displays
the pathway highlighting EC's that are "missing" from the subsystem
and should perhaps be added.  (Note: KEGG uses the color red for
highlighting).  If you open both of these links in two separate
browser tabs, you can switch between them and see the differences in
highlighting.  This gives you a view on how the subsystem
overlaps with the pathway and provides all the information you need to
click on those EC's and find more about them, or possibly add them to your
subsystem.  Any changes made using the subsys_hope.cgi webpage to a
subsystem are reflected in the regular subsys.cgi page.
pathway.cgi enables a global assessment of the coverage of KEGG pathways by the subsystems in SEED.
<h2>Installing KEGG XML files</h2>
<li>Information on the KEGG XML file format can be found <a href=http://www.genome.jp/kegg/xml/>here</a>.
<li>Open an FTP connection to acquire the <a href= ftp://ftp.genome.jp/pub/kegg/xml>Reference Metabolic and Regulatory Pathways</a>.
<li>Navigate to the KGML_v0.6/map directory. Copy this entire directory to a directory on FIGdisk (e.g., "FIG/Data/KGML/maps/").
<li>For the SEED to be able to use the files, you need to configure its knowledge of the directory they are stored in.  Open the FIG_Config.pm module, and add an entry with the following format: $kgml_dir = "&lt;Directory Path to KGML maps folder&gt;".

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