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License: GNU General Public License v2.0
Make sense of omics data with graph database + mining + visualization.
License: GNU General Public License v2.0
perhaps need to output to gephi then to igraph?
Try to initialise a metabolic reaction bipartite graph as a DB and we link out from there.
currently the data is listed as below:
ko -> cpd -> ko
XML
R00001: C00404 + n C00001 <=> (n+1) C02174
filepath: kegg_dump/ligand/reaction/reaction.lst (eqn) or reaction (rxn name & details)
filepath: kegg_dump/ligand/compound/compound (names, id & details)
::More information::
perl -0777 -ne '@A=split(qq(///),$_); END{print $a[1]}' ligand/reaction/reaction
ENTRY R00002 Reaction
NAME Reduced ferredoxin:dinitrogen oxidoreductase (ATP-hydrolysing)
DEFINITION 16 ATP + 16 H2O + 8 Reduced ferredoxin <=> 8 e- + 16 Orthophosphate + 16 ADP + 8 Oxidized ferredoxin
EQUATION 16 C00002 + 16 C00001 + 8 C00138 <=> 8 C05359 + 16 C00009 + 16 C00008 + 8 C00139
COMMENT a part of multi-step reaction (see R05185, R00002+R00067+R00153+R02802+R04782)
RPAIR RP00003 C00002_C00008 main
RP00010 C00002_C00009 leave
RP05676 C00001_C00009 leave
ENZYME 1.18.6.1
rxns2KOs
every enz/KO comes with a list of associated reactions
filepath: /export2/home/uesu/kegg_dump/genes/ko/ko
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