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

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

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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