Re: [XMLPipeDB-developer] Plasmodium bug/task list

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I'm down in the bio lab at the moment looking at this.

I understand what needs to be done in regards to 1) keeping all ORF id's and
then 2) querying the id's with underscores to then remove the underscores
but maintaining the original underscore id's.

I performed an export with the pattern match as-is and commented out the
exclude 'ordered locus' and 'ORF'. The export completed but with only 5110
gene id's. So it seems we are missing 235 gene id's that are in the XML
file as seen from the raw sql query.

Based on Dr. D's analysis of a missing pattern of PFA_####[aw] I went ahead
and added it into the pattern match string and called it as the others are
called in the query. Once the export completes I'll confirm that in fact we
have captured all the id's. Once confirmed, I will move onto the query to
find id's with underscores and handle them as mentioned above.

Richard
On Thu, Mar 17, 2011 at 7:34 AM, Richard Brous <rbr...@gm...> wrote:

>  Thanks for info. I will dig into this after my 10 am exam tomorrow.
>
> Richard
>
> Sent from my iPhone
>
> On Mar 16, 2011, at 4:18 PM, Kam Dahlquist <kda...@lm...> wrote:
>
>  Hi,
>
> More information on the underscore issue:
>
> There is an ID with the pattern
>
> PFA_[0-9][0-9][0-9][0-9][wc]
>
> that needs to have the underscore removed so that reads instead
>
> PFA[0-9][0-9][0-9][0-9][wc]
>
> I don't know why these IDs exist in UniProt, but in PlasmoDB, they are
> there without the underscore and won't be recognized with it.  I think we
> should leave the underscore ones there, but also have a set without the
> underscore.  There are 134 records that have this issue.
>
> If Rich can make these two fixes (capturing the ORFs and dealing with the
> underscore), then I think we will be good to go with Plasmodium.  There may
> be code in the Vibrio or Helicobacter profiles to help with the underscores,
> but I'm not sure.
>
> Best,
> Kam
>
> At 02:59 PM 3/16/2011, Kam Dahlquist wrote:
>
> Hi,
>
> I've taken a look at the list of IDs and did a quick comparison with both
> the older released gdb and also a list I downloaded from the Broad Institute
> Plasmodium database.  I think we can safely go with the query on the ORF tag
> for our export--all of those different ID forms are valid.  There are about
> 400 IDs that are different in the older released gdb than in the new query;
> I'm going to further investigate those.  I suspect that the difference is
> mainly due to a +/- underscore issue that we might need to solve.  However,
> we should go forward with capturing all the IDs from the ORF tag, I don't
> see a need to restrict to a particular pattern there.
>
> Best,
> Kam
>
> At 09:48 PM 3/14/2011, you wrote:
>
> Hi all,
>
> So I went ahead and did raw sql queries of the Postgres data and turned up
> the following:
>
> select * from genenametype where type = 'ordered locus'
> Returned zero gene ids
>
> select * from genenametype where type = 'ORF'
> Returned 5345 gene ids
> The type = 'ORF' query was exported into excel and posted to the biodb wiki
> on the Spring 2011 Plasmodium page.
>
> There are many many patterns in regards to gene ids, here the the prefixes
> from my cursory look:
> MAL
> PF##_
> PFA
> PFB
> PFC
> PFD
> PFE
> PFF
> PFI
> PFL
>
> Richard
>
>
> On Mon, Mar 14, 2011 at 10:32 AM, Kam Dahlquist <kda...@lm...>
> wrote: Hi,
> I looked up an assortment of IDs in UniProt and I can confirm that it
> appears that the IDs are found in the ORF tag, not the OrderedLocus tag
> (except for the one that got captured in the export).
> Best, Kam
>
> At 08:09 AM 3/14/2011, you wrote:
>
> 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 > > >
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