Re: [XMLPipeDB-developer] H pylori generic profile issue gmb2b71

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

Hi,

Let's go ahead and make these changes.  I'll need to run the exports 
and validate the gdb's, of course, but I think this will be better so 
that I can actually test the custom profiles.

We don't need to do the forensics on what happened, but I don't ever 
recall specifically calling out the taxon IDs that needed to be put 
in the code, so maybe Rich just looked them up online and guessed.

Best,
Kam

At 12:59 PM 11/25/2013, you wrote:
>Greetings,
>
>Here are my cross-reference results.  It turns out there were a 
>couple more discrepancies; the rest match.  Not sure where the 
>incorrect IDs came from at this point, but here are the pending changes:
>
>- H. pylori, code: 210; wiki: 85962
>- P. aeruginosa, code: 287; wiki: 208964
>- S. typhimurium, code: 90371; wiki: 99287
>
>Finally, the wiki notes that M. tuberculosis is 83332 but has 
>changed to 1773; the code already has 1773 for that species profile, 
>so presumably this can be left as is.
>
>If these changes look good (i.e., code will be changed to match the 
>wiki), then I'll send up a new release.
>
>John David N. Dionisio, PhD
>Associate Professor, Computer Science
>Associate Director, University Honors Program
>Loyola Marymount University
>
>
>
>On Nov 25, 2013, at 11:31 AM, John David N. Dionisio <do...@lm...> wrote:
>
> >
> > OK, I will do a cross-check.  It's certainly possible that the 
> wrong taxon IDs were mentioned; on the side I can check the version 
> histories to see where things went wrong.
> >
> > But the main task is to check the code taxon IDs with the ones on 
> that page.  I'll make corrections then release a new version.
> >
> > John David N. Dionisio, PhD
> > Associate Professor, Computer Science
> > Associate Director, University Honors Program
> > Loyola Marymount University
> >
> >
> >> On Nov 25, 2013, at 9:16 AM, Kam Dahlquist <kda...@lm...> wrote:
> >>
> >> Hi,
> >>
> >> I don't know how 210 became the taxon ID in the code.  I checked the
> >> ReadMe for the released version of the gdb and the tax ID for that
> >> version is 85962.
> >>
> >> I've gone through all the ReadMe's to double-check the tax IDs that I
> >> have listed on my user page on the BiolDB wiki
> >> here:
> >> 
> https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/User:Kdahlquist#UniProt_XML
> >>
> >> I only anticipate issues with changing tax IDs for E. coli,
> >> Arabidopsis, and Mycobacterium tuberculosis.
> >>
> >> Is it possible that when Rich (I think it was him) made the change to
> >> putting in tax IDs instead of species names, he put in the wrong tax
> >> ID?  If so, it's probably worth it to check all the tax IDs for the
> >> custom profiles and make sure they match what I have put on that
> >> page.  I think there may be issues with E. coli, Arabidopsis, and M.
> >> tuberculosis, though.
> >>
> >> Best,
> >> Kam
> >>
> >> At 11:37 PM 11/22/2013, you wrote:
> >>> I checked the custom species profile in our code and the taxon ID
> >>> that is associated with H. pylori is 210.  This may be another case
> >>> of a changed taxon ID, seeing as the data reports 85962 instead, as
> >>> seen in your attached screenshots.
> >>>
> >>> John David N. Dionisio, PhD
> >>> Associate Professor, Computer Science
> >>> Associate Director, University Honors Program
> >>> Loyola Marymount University
> >>>
> >>>
> >>>
> >>>> On Nov 22, 2013, at 4:45 PM, Kam Dahlquist <kda...@lm...> wrote:
> >>>>
> >>>> Hi,
> >>>>
> >>>> Just started an export of H. pylori.  There were two profiles
> >>> that showed up, both with the same taxon ID, both said they were
> >>> generic profiles.  I'm attaching 2 screenshots.
> >>>>
> >>>> Best,
> >>>> Kam
> >>> 
> <gmb2b71_export_genericprofile1.jpg><gmb2b71_export_genericprofile2.jpg>------------------------------------------------------------------------------
> >>>> Shape the Mobile Experience: Free Subscription
> >>>> Software experts and developers: Be at the forefront of tech innovation.
> >>>> Intel(R) Software Adrenaline delivers strategic insight and 
> game-changing
> >>>> conversations that shape the rapidly evolving mobile landscape.
> >>> Sign up now.
> >>>> 
> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
> >>>> _______________________________________________
> >>>> xmlpipedb-developer mailing list
> >>>> xml...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>>
> >>>
> >>> 
> ------------------------------------------------------------------------------
> >>> Shape the Mobile Experience: Free Subscription
> >>> Software experts and developers: Be at the forefront of tech innovation.
> >>> Intel(R) Software Adrenaline delivers strategic insight and game-changing
> >>> conversations that shape the rapidly evolving mobile landscape. 
> Sign up now.
> >>> 
> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
> >>> _______________________________________________
> >>> xmlpipedb-developer mailing list
> >>> xml...@li...
> >>> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >>
> >>
> >> 
> ------------------------------------------------------------------------------
> >> Shape the Mobile Experience: Free Subscription
> >> Software experts and developers: Be at the forefront of tech innovation.
> >> Intel(R) Software Adrenaline delivers strategic insight and game-changing
> >> conversations that shape the rapidly evolving mobile landscape. 
> Sign up now.
> >> 
> http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
> >> _______________________________________________
> >> xmlpipedb-developer mailing list
> >> xml...@li...
> >> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> > 
> ------------------------------------------------------------------------------
> > Shape the Mobile Experience: Free Subscription
> > Software experts and developers: Be at the forefront of tech innovation.
> > Intel(R) Software Adrenaline delivers strategic insight and game-changing
> > conversations that shape the rapidly evolving mobile landscape. 
> Sign up now.
> > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
>
>------------------------------------------------------------------------------
>Shape the Mobile Experience: Free Subscription
>Software experts and developers: Be at the forefront of tech innovation.
>Intel(R) Software Adrenaline delivers strategic insight and game-changing
>conversations that shape the rapidly evolving mobile landscape. Sign up now.
>http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk
>_______________________________________________
>xmlpipedb-developer mailing list
>xml...@li...
>https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer