how I can edit the different comparments of my PGDB

edit

Hi Beatriz,

CCO-PM-BAC-NEG is the plasma membrane for a Gram-negative bacterium (if your organism is not a Gram-negative bacterium, you probably shouldn't have this compartment -- you should have the corresponding compartment for Gram-positive bacteria instead, but if you're seeing this as the location of a transport reaction, it probably means that the reaction was originally defined in MetaCyc for a Gram-negative bacterium and used the specific compartment instead of a generic one).

CCO-CYTOSOL is of course the cytosol.

CCO-IN, CCO-OUT and CCO-MIDDLE are generic compartments used to describe reactions that cross one or two unspecified membranes. In general, for a Gram-negative bacterium, CCO-IN and CCO-OUT will correspond to cytosol and periplasm respectively for reactions that cross the plasma membrane, and periplasm and extracellular respectively for reactions that cross the outer membrane, though they could also correspond to cytosol and extracellular, in which case CCO-MIDDLE would correspond to the periplasm.

There are a number of other compartments you haven't mentioned here (including CCO-EXTRACELLULAR), presumably because you haven't come across them.

CCO-OUT-CCO-IN and T are not actual valid compartments. I'm not entirely sure, but I assume T refers to a default of some kind (which will presumably map to cytosol), and CCO-OUT-CCO-IN is used for some transport reactions to refer to some unspecified membrane or set of membrane and spaces between the in and out compartments.

You can explore the full CCO ontology at http://brg.ai.sri.com/CCO/ (though I'm not sure how up-to-date it is). The vast majority of these terms are for eukaryotes, however, and will not be relevant for prokaryotes. If you invoke the protein editor for some protein in your PGDB, and click on the button to edit Cellular Component GO Terms, the left-hand pane of the resulting pop-up shows all the specific compartments (i.e. excluding CCO-IN, etc.) that are instantiated in your organism, and which GO terms they correspond to. The ids for most of these terms may differ from the ones you listed above -- if they start with CCI instead of CCO, then they are specific instances of the corresponding CCO class terms.

You do have some limited ability to update the set of compartments in your PGDB. If you open pathologic and invoke the command Refine -> Update Cellular Architecture, you can specify what structures are present/absent in your organism, but there is not necessarily a one-to-one correspondence between listed structures and CCO terms (in particular, a given organelle will have CCO terms for each of its membranes and spaces). I'm guessing you probably won't want to make any changes here, however, and regardless, I don't know that any changes you make would have any impact on MetaFlux. If you invoke the Reaction Editor on some reaction, you can assign compartments for the reaction substrates (either generic or specific but spaces only, not membranes) -- this may impact how the reaction is treated by MetaFlux, I'm not sure.

I personally do not know ... (more)