Preliminary results from integrating iJR904 and EcoCyc compounds...
zucker
Alan Ruttenberg and I have taken the iJR904 and EcoCyc compounds and
converted them to BioPAX/OWL so that they can be directly compared and
checked for inconsistencies using the description logic reasoners. The
details of our methodology can be found here:
http://www.freebiology.org/wiki/Debugging_the_bug#Methodology
The main results can be found here:
http://www.freebiology.org/wiki/Debugging_the_bug#Bugs_found_comparing_EcoCyc_compounds_to_iJR904_compounds
The bugs found in iJR904 can be found here:
http://www.mumble.net/~alanr/FBA_model-1-12-06-compounds.patches
and the bugs found in EcoCyc can be found here:
http://www.mumble.net/~alanr/EcoCyc-compounds-2006-02-16.patches
The next steps are to review the semi-automated mappings that Markus and
Ingrid performed, and see where further opportunities for making
correspondences are. Next, we will begin to translate reactions and get
matches between them.
Sincerely,
Jeremy and Alan