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

[John D. N. D. <do...@lm...>]

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>------------------------------------------------------------------------------
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