Re: [XMLPipeDB-developer] GenMAPP multitaxon support - CMSI 486T

[Richard B. <rbr...@gm...>]

Ok, well if I could hazard a guess I would say that only the GO associations
that relate to the particular species are included. The code looks for an
association of a GO term then exports it. If no association then skips to
the next Go term... rinse and repeat?

If this is the case then we would need to iterate the validation of GO terms
for each species. The other question would be ... can we build the GO table
in multiple passes( if two or more species use a common GO term, are the
earlier records overwritten ) ?

I'm sure Dondi will know but I'll spend some time rereading the code myself.

Richard

On Thu, Aug 4, 2011 at 1:00 PM, Kam Dahlquist <kda...@lm...> wrote:

> Hi,
>
> Dondi will have to chime in on this, but I think this is where things are
> going to get tricky.
>
> The final gdb does not actually contain the entire GO, it gets trimmed
> somehow based on the GO associations for a particular species.  This is
> because MAPPFinder cannot handle loading the entire GO.  Since there is some
> type of species-specific trimming going on, it's quite possible that this
> will need to iterate.
>
> However, I don't have the foggiest idea of how this works, so Dondi will
> have to chime in.
>
> Best,
> Kam
>
>
> At 12:09 AM 8/4/2011, you wrote:
>
> Wednesday 8/3/11 progress:
>
> 1. After following the ExportPanel1.java ground zero code of:
> databaseProfile.setSelectedSpeciesProfile( selectedProfile );
>
> I found the method in DatabaseProfile.java plus a getter method;
> SpeciesProfile setSelectedSpeciesProfile( speciesProfile ) and
> SpeciesProfile getSelectedSpeciesProfile( speciesProfile )
>
> I created two new methods that each handle List<Object> of SpeciesProfiles
> argument instead of a single SpeciesProfile; setSelectedSpeciesProfiles and
> getSelectedSpeciesProfiles.
>
> This enabled the ExportPanel1 ground zero code to become:
> databaseProfile.setSelectedSpeciesProfiles(selectedSpecies);
>
> 2. public static void export() on line 104 in ExportToGenMAPP.java
>
> On line 107 ExportGoData is instantiated which I found in ExportGoData.java
> and calls a method: *public* *void* export(*char* chosenAspect, *int*taxon).
>
> Within export, taxon id is required for another method: *private* *void*populateGoTables(
> *char* chosenAspect, *int* taxon).
>
> Within populateGoTables, taxon id is required for another method: *private
> * *void* populateUniprotGoTableFromSQL(* char* chosenAspect, *int* taxon).
>
> But, if the export to GDB process starts off with exporting GO data,
> doesn't it only need to do that once no matter how many species are
> selected? As you probably realize, I'm leading towards not having to iterate
> through this for each taxon id if possible.
>
> Also, how does the export actually work? How are GO ids and UniProt ids
> related within the table?
>
> Thanks!
>
> Richard
>
>
>
>
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