Re: [XMLPipeDB-developer] UniProt_All issues

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

Yes, it seems that the species filtering did not go all the way to the relationship exporting code.  I will have to look at this more closely.

Wow---47 GB compressed...now *that* is getting to "big data."  And I agree it will probably not end up exporting a match for our needs.

John David N. Dionisio, PhD
Associate Professor, Computer Science
Associate Director, University Honors Program
Loyola Marymount University



On Jul 1, 2014, at 2:28 PM, Dahlquist, Kam D. <Kam...@lm...> wrote:

> Hi,
> 
> The export of H. pylori from the UniProt_All postgres database crashed at the relations tables.  It was stuck and I clicked the cancel button and the Fatal error message came up shown on the wiki here:
> 
> http://xmlpipedb.sourceforge.net/wiki/index.php/Kdahlquist#2014-06-27
> 
> I also note that the UniProt table had only about 500 records when ~1500 were expected (judging by the single-proteome export).  I am sure this is because the TrEMBL records were missing.  I looked into downloading TrEMBL, but it is ~47 GB compressed!  Even if we wanted to deal with that large of a file, chances are that an export from that would have many more records than the proteome and not be suitable for our needs.
> 
> So it looks like we are stuck with the single species proteomes for now.
> 
> However, we should maybe still look into this bug because it might potentially affect other exports when multiple species are loaded.
> 
> I was thinking that I might start loading multiple species' proteomes into the same postgres database so that I don't have to keep loading/processing GO all the time.
> 
> Best,
> Kam
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