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

[Kam D. <kda...@lm...>]

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