Re: [XMLPipeDB-developer] M smeg source data files?

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

Leaving for LMU now, can you please open up the computer lab for me?

On Wed, Mar 2, 2011 at 11:09 AM, Richard Brous <rbr...@gm...> wrote:

> Heading down there in an hour or so. Need to use that Mac as I've come as
> farces I can on my laptop.
>
> Richard
>
> Sent from my iPhone
>
> On Mar 1, 2011, at 4:09 PM, Kam Dahlquist <kda...@lm...> wrote:
>
> > Hi,
> >
> > I've got an update on this.
> >
> > I went an retrieved the source files from the Mac Rich was using in
> > Seaver 120.  It appears that while the 11/28/10 versions of the
> > source files were uploaded to the wiki, the 11/16/10 versions of the
> > files were the ones actually used to export the deliverable gdb.
> >
> > This doesn't affect the versioning info on the ReadMe for the UniProt
> > XML because that is only updated once a month and appears to be the
> > same file on both of the above dates.  However, both the GO and GOA
> > files are different.  We do not have the version info for the 11/1610
> > GO OBO-XML file (at least I don't know where it is).  And the version
> > info for the GOA file in the ReadMe is incorrect, it is not reporting
> > the right information for GOA, but is repeating what was said for the
> > UniProt XML.
> >
> > So at this point, we can't release the M. smegmatis gdb until we get
> > the versioning issues resolved and are sure that the readme is correct.
> >
> > I decided to try downloading fresh source files and just
> > importing/exporting a new gdb.  However, the GO OBO-XML gave an
> > error.  Either this particular GO file is bad or there is a change in
> > the format.  I'm going to put this to the side for now until I can
> > work with Rich to resolve the above versioning issues and move on to
> > working on the other gdb's.
> >
> > I've been annotating the task list on the wiki with my progress.
> >
> >
> https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=Task_List
> >
> > Best,
> > Dr. D
> >
> > At 06:52 PM 2/28/2011, Kam Dahlquist wrote:
> >> Hi Rich,
> >>
> >> I ran an export of the Mycobacterium smegmatis gdb today with the
> >> data source files (UniProt XML, GO OBO-XML, GOA) found on the A team
> >> deliverables page.  However, I didn't get the same number of GO
> >> terms that you did when you last exported an M smeg gdb on
> >> 2011-01-28 or as your team turned in for the deliverables.  the 1/28
> >> version was identical to the deliverables version, but my version
> >> had a different number of GO terms.  I wanted to double-check with
> >> you that those were the correct GO XML and GOA files to use.
> >>
> >> Thanks,
> >> Dr. D
> >
> >
> >
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