Reaction locations in/out to cytosol/extracellular space

asked 2017-11-24 05:39:47 -0500

johnepearl gravatar image

Hi Pathway Tools,

I'm hope you can give me some advice on how to handle reaction locations.

When I make a new PDGB from a GB file using Pathologic, some of the reaction locations [shown in the Edit Reaction dialog box] default to 'in' or 'out' -- these seem to be the ones that are involved in transport reactions or electron transport.

Can you recommend a search strategy that would identify all reactions with locations that are in/out? In web server mode, the advanced search comes close, but reaction location is not listed under the Where field.

Next, can you suggest how I might globally replace 'in' with 'cytosol' and 'out' with 'extracellular space'?

I'm aware that I can export an SBML version of the PDGB to use the COBRAToolbox in MATLAB to find and fix these reaction locations, but this seems needlessly complicated.

It would be great if this global in/out to cytosol/extracellular space replacement could be made a feature of the Consistency Checker.

Thanks, keep up the excellent work, John at the University of Leicester, UK

PathwayTools v21 on Win7x64 Ent

edit retag flag offensive close merge delete