Re: [XMLPipeDB-developer] Plasmodium bug/task list
Brought to you by:
kdahlquist,
zugzugglug
Menu
▾
▴
Re: [XMLPipeDB-developer] Plasmodium bug/task list
|
From: Richard B. <rbr...@gm...> - 2011-03-14 15:09:33
|
Thanks Dondi,
Will review this after our call today. I have been a little worried as the
DEBUG export has been going for 2.5 days with progress at 65% and 6.5 Gb of
log files so far... /yikes
Btw I have a work lunch meeting in Beverly Hills today so will be working
from home afterwards instead of in the bio lab.
Richard
On Sun, Mar 13, 2011 at 9:55 PM, John David N. Dionisio <do...@lm...>wrote:
> Thanks for the updates, Rich.
>
> I gave things a once-over and may have a lead. Here is what I found:
>
> - First, the TallyEngine customization for P. falciparum states the
> following:
>
>
> # Plasmodium falciparum
> plasmodiumfalciparum_level_amount=2
>
> plasmodiumfalciparum_element_level0=uniprot/entry/gene/name&type&ORF
> plasmodiumfalciparum_element_level1=uniprot/entry/gene/name&type&UniGene
>
> plasmodiumfalciparum_query_level0=select count(*) from genenametype where
> type = 'ORF';
> plasmodiumfalciparum_query_level1=select count(*) from genenametype where
> type = 'UniGene';
>
> plasmodiumfalciparum_table_name_level0=Ordered Locus
> plasmodiumfalciparum_table_name_level1=UniGene
>
>
> Thus, what is being counted by TallyEngine as "Ordered Locus" are the gene
> names whose type is 'ORF' ("level0" properties).
>
> - Now, this is what the P. falciparum species profile does when harvesting
> IDs
> (PlasmodiumFalciparumUniProtSpeciesProfile.getSystemTableManagerCustomizations):
>
>
> String sqlQuery = "select d.entrytype_gene_hjid as hjid, c.value " +
> "from genenametype c inner join entrytype_genetype d " +
> "on (c.entrytype_genetype_name_hjid = d.hjid) " +
> "where (c.value similar to ? " +
> "or c.value similar to ? " +
> "or c.value similar to ?) " +
> "and type <> 'ordered locus names' " +
> "and type <> 'ORF' " +
> "group by d.entrytype_gene_hjid, c.value";
>
>
> Note the condition on the second-to-last line --- the query actually
> *omits* gene names whose type is 'ORF'! So the question is...which is
> right? (I'm inclined to believe the Tally Engine here, since, the export
> puts only one record in OrderedLocusNames)
>
> Still, comparing these two queries directly against the PostgreSQL database
> would be educational, I think. Then, knowing which criteria are correct,
> the appropriate action can then be taken, I think.
>
> Hope this helps...
>
> John David N. Dionisio, PhD
> Associate Professor, Computer Science
> Loyola Marymount University
>
>
>
> On Mar 12, 2011, at 9:48 AM, Richard Brous wrote:
>
> > Debug export is still going... 2.5GB of log files so far with progress at
> 65%...
> >
> > I posted the link of the WARN log on the plasmodium page here:
> https://www.cs.lmu.edu/biodb/fall2010/index.php/Plasmodium_falciparum.
> > Richard
> > On Fri, Mar 11, 2011 at 1:06 PM, Richard Brous <rbr...@gm...>
> wrote:
> > Hi all,
> >
> > Have been working through several Plasmodium gdb exports in an attempt to
> source why only one gene id makes it into the Ordered Locus table.
> >
> > I have reviewed the logger file while set to "WARN" and wasn't able to
> determine anything which would suggest an error. I will post this log file
> to the wiki later today when I get home.
> >
> > I then upped the logger verbosity to "DEBUG" and file size to 100MB with
> hopes that more detail will surface the issue, but my export is on hour 20
> and still going (although its nearly complete). What I didn't expect was the
> size of the log files and that it seems only the last 3 are kept with
> earlier logs being overwritten =( I fear that the information I need it in
> one of the earlier files which are now lost.
> >
> > Unless a better suggestion is offered I'm going to rerun an export again
> with 'DEBUG" verbosity and up the file sizes to near 1 GB each and hope that
> 3 GB total will be enough to hold the complete export log.
> >
> > More info as it comes...
> >
> > Richard
> >
> >
> >
> >
> >
> > On Fri, Mar 4, 2011 at 3:17 PM, Kam Dahlquist <kda...@lm...>
> wrote:
> > Hi,
> >
> > I've completed testing the Plasmodium gdb I exported last November and
> updated the SourceForge wiki.
> >
> > Plasmodium has it's own task list page, which I've updated here:
> https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=Plasmodium_falciparum_Task_List
> >
> > The testing report can be found here:
> https://sourceforge.net/apps/mediawiki/xmlpipedb/index.php?title=Gene_Database_Testing_Report_P._falciparum_20101115
> >
> > The source files and gdb are on a new Plasmodium falciparum page on the
> Fall 2010 BiolDB wiki:
> https://www.cs.lmu.edu/biodb/fall2010/index.php/Plasmodium_falciparum
> >
> > Here is the list of bugs/action items that I've listed:
> >
> > 1. The OrderedLocusNames table in the gdb only has 1 ID out of 5345
> repored by the TallyEngine. This also affects all other tables related to
> OrderedLocusNames.
> >
> > 2. The GeneId table in the database has 6 fewer IDs than reported by the
> TallyEngine (Mycobacterium smegmatis and Mycobacterium tuberculosis also
> have mysterious GeneId issues with the TallyEngine).
> >
> > 3. The count for EMBL IDs in the gdb also seems low, it's lower than the
> 2009 version of the gdb. There's no way to tell at this point whether this
> is due to a change in annotation by UniProt or is a bug with GenMAPP
> Builder.
> >
> > Thanks,
> > Kam
> >
> >
> >
> ------------------------------------------------------------------------------
> > What You Don't Know About Data Connectivity CAN Hurt You
> > This paper provides an overview of data connectivity, details
> > its effect on application quality, and explores various alternative
> > solutions. http://p.sf.net/sfu/progress-d2d
> > _______________________________________________
> > xmlpipedb-developer mailing list
> > xml...@li...
> > https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
> >
> >
> >
> > <ATT00001..txt><ATT00002..txt>
>
>
>
> ------------------------------------------------------------------------------
> Colocation vs. Managed Hosting
> A question and answer guide to determining the best fit
> for your organization - today and in the future.
> http://p.sf.net/sfu/internap-sfd2d
> _______________________________________________
> xmlpipedb-developer mailing list
> xml...@li...
> https://lists.sourceforge.net/lists/listinfo/xmlpipedb-developer
>
|
