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

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

Sounds good. Will document the issues and release the files when they are
available.

Richard

On Thu, Mar 3, 2011 at 2:19 PM, Kam Dahlquist <kda...@lm...> wrote:

> Hi,
>
> I have resolved any outstanding issues for Mycobacterium smegmatis.
>
> 1.  The import/export I completed with the 11/28 version of files retrieved
> from the S120 Mac matched with both the 20101130 and 20110128 versions of
> the gdb.  Thus, it was  a mistake with the version of the source files
> posted to the A-team page, but it  *WAS* the 11/28 versions that were used
> to generate the gdb's.
>
> 2.  I was able to correctly state the version of the source files for the
> ReadMe; we are going to release the 20110128 version (with the corrected
> link-out).
>
> 3.  There is an issue with the TallyEngine for M. smegmatis with regards to
> the number of RefSeq and GeneIds.  TallyEngine reports 6720 for both the XML
> and database, while there are only 6716 in the gdb.  I ran match on the XML
> for the pattern for RefSeq and GeneId and found that there are only 6716 of
> each of those IDs in the XML.  So I don't know why there are four extra
> being counted by the TallyEngine.  Since this is only affecting the
> TallyEngine and not the gdb, I think we are OK to release.  I'm going to
> send the files in a separate e-mail.
>
> Cheers,
> Kam
>
>
>
>
>  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
>
>
>
> ------------------------------------------------------------------------------
> What You Don't Know About Data Connectivity CAN Hurt You
> This paper provides an overview of data connectivity, details
> its effect on application quality, and explores various alternative
> solutions. http://p.sf.net/sfu/progress-d2d
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>