gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] PostgreSQL Version

[Michael S. <msa...@pc...>]

Hi Alberto,

Thanks for your interest.  Here's a brief overview of what we've been up 
to with respect to the PostgreSQL version.  Currently, the official GUS 
schema is contained within our instance here at CBIL.  From time to 
time, we use custom scripts to extract the schema, and release versions 
of GUS.  With the PostgreSQL release, we'd like to turn this model on 
its head, maintaining instead the canonical version of GUS as an XML 
representation, and then using that XML to either generate Oracle or 
PostgreSQL installation scripts and DDL.

We're using a package called SQLFairy (SQL::Translator) to assist in 
this process-- it has much of the functionality we require, but not 
quite all.  Thus, I've been working with the SQLFairy group to make the 
necessary changes.  So far, the Oracle parser has been reimplemented, 
and I'm very close to producing the canonical XML file which will 
represent GUS.  (My goal is to complete this by the end of the week). 
Once the XML document has been created, some work will be necessary to 
modify the Oracle and PostgreSQL producers, which will then allow for 
end-to-end Oracle DLL-> XML -> Oracle/PostgreSQL DDL in a programmatic 
fashion.

Assuming all goes well this week with the Oracle Parser, I hope to 
complete the Producer changes the following week, and address any 
bugs/issues.  So hopefully by mid-September we'll be ready with this 
stuff.  Of course, as you can assume from my earlier time estimate, this 
is only a rough guess, and as other projects require diversions of my 
attention, this will affect the timeline.

If your student is familiar with Perl and is interested, they are more 
than welcome to help with modifying SQLFairy to accomplish this. 
Eventually everything will be committed back to the main SQLFairy CVS, 
but they're on the cusp of a release and so I'm holding off adding my 
changes for now.

Thanks,

Mike

Alberto Davila wrote:

> Dear Mike,
> 
> I have a student here that will center efforts to try to use GUS with
> PostgreSQL. If that GUS version has been released, would you kindly let
> us know from where we can download ? Otherwise, any data/doc you may
> have on it and able to share would be greatly appreciated.
> 
> Thanks, Alberto
> 
> 
> On Thu, 2004-08-12 at 10:46, Michael Saffitz wrote:
> 
>>Hello Jeetendra,
>>
>>We're actively working on the PostgreSQL version of GUS, and I hope to 
>>release late next week.
>>
>>We have a proof of concept version in place, and we're just now working 
>>to integrate this with our installation and configuration framework.
>>
>>Thanks,
>>
>>Mike
>>
>>On Aug 11, 2004, at 4:57 PM, Jeetendra Soneja wrote:
>>
>>
>>>Any idea on when the PostgreSQL version of GUS is expected to be 
>>>released?
>>>
>>>~Jeetendra.
>>>
>>>

Re: [Gusdev-gusdev] PostgreSQL Version

[Alberto D. <da...@io...>]

Dear Mike,

I have a student here that will center efforts to try to use GUS with
PostgreSQL. If that GUS version has been released, would you kindly let
us know from where we can download ? Otherwise, any data/doc you may
have on it and able to share would be greatly appreciated.

Thanks, Alberto


On Thu, 2004-08-12 at 10:46, Michael Saffitz wrote:
> Hello Jeetendra,
> 
> We're actively working on the PostgreSQL version of GUS, and I hope to 
> release late next week.
> 
> We have a proof of concept version in place, and we're just now working 
> to integrate this with our installation and configuration framework.
> 
> Thanks,
> 
> Mike
> 
> On Aug 11, 2004, at 4:57 PM, Jeetendra Soneja wrote:
> 
> > Any idea on when the PostgreSQL version of GUS is expected to be 
> > released?
> >
> > ~Jeetendra.
> >
> >

[Gusdev-gusdev] new plugin for RAD

[Elisabetta M. <man...@pc...>]

A new plugin is now available from the Sanger cvs repository: the 
BatchArrayResultLoader. All the supporting utilds an  Documentation is 
available at 
http://www.gusdb.org/documentation/plugins/GUS-RAD-Plugin-BatchArrayResultLoader.html
This plugin can be used to load *in batch* quantification results from 
any of Affymetrix MAS 4.0, Affymetrix MAS 5.0, RMAExpress, GenePix, 
ArrayVision into RAD.
Note, this plugin was previously in the CBIL cvs repository as it contains 
some hard-coded parts which are specific of our database instance. 
However, see the section 'NOTES: Warning' of the above documentation for 
information on how to modify the plugin to make it compatible with your 
own instance of the database.
Elisabetta

Re: [Gusdev-gusdev] dots.nagene to dots.gene

[Chris S. <sto...@pc...>]

Hi Jinal,
Thanks for bringing this up. I have started looking into this and hope 
to have some plans to report soon.
Cheers,
Chris

On Aug 25, 2004, at 5:47 PM, Jinal Jhaveri wrote:

> On the other note, I remember Steve mentioning about plans to arrange 
> a GUS
> Users Meeting in PCBI, in one of the mails. IMHO It would be great if 
> we can
> have that as I know atleast of 3 to 4 more groups (at Virginia 
> Bioinformatics
> Institute)  are planning to use GUS and everyone is waiting for a GUS 
> User
> Meeting like this where we can clear our doubts and become more 
> efficient to
> handle it for our projects. I am sure other groups too will be 
> interested in
> joining this. Any thoughts/comments on the plan ?
>
Chris Stoeckert, Ph.D.
Research Associate Professor, Dept. of Genetics
1415 Blockley Hall, Center for Bioinformatics
423 Guardian Dr., University of Pennsylvania
Philadelphia, PA 19104
Ph: 215-573-4409 FAX: 215-573-3111

RE: [Gusdev-gusdev] dots.nagene to dots.gene

[Y. T. G. <yg...@pc...>]

Hi Jinal, 
Your plan sounds reasonable to me. As for the question regarding
RnaInstance,
it is parallel to GeneInstance. You just need to make a
RnaInstanceCategory entry
(we have 0: unknown, 1: mRNA, 2: assembly <of ESTs>), make RnaInstance
entries
to be associated with this category and with RNAs. Also make RnaFeature
using info
such as rna name, number of exons to be attached to your RnaInstance.

-Thomas

> -----Original Message-----
> From: gus...@li... 
> [mailto:gus...@li...] On Behalf 
> Of Jinal Jhaveri
> Sent: Thursday, August 26, 2004 11:12 AM
> To: gus...@li...
> Cc: yg...@pc...
> Subject: Re: [Gusdev-gusdev] dots.nagene to dots.gene
> 
> 
> 
> Thanks Thomas,
> 
> You reply was really helpful. I was thinking on the same 
> track. Here is what I 
> am planning to do. I already have one of my genomes annotated 
> (and submited 
> to genbank. And I was thinking of generating gbk files for 
> the other genomes 
> and submit it to gus using gbparser). So following are the steps I am 
> planning to take
> 
> 1) Parse the genbank file and thus I will have most of my na 
> tables filled
> 2) Fill the geneinstance and the gene tables and connect 
> geneinstance to 
> nafeatureimp using na_feature_id
> 3) Fill the aa_featureimp table and connect it to nafeatureimp using 
> na_feature_id
> 4) Fill the RNA table(just ids) and connecting it to gene table 
> 5) Fill the protein_instance table connect it to aafeatureimp through 
> aa_feature_id table
> 6) Fill the protein table and establish relation with RNA 
> using rna_id and  
> ofcourse with protein_instance
> 
> One thing which isn't clear is how will I fill in the 
> rnainstance table. How 
> can this information be available from ncbi genbank? Well I 
> understand that I 
> can ignore it for a while and just generate fake rna_ids just 
> to establish 
> connection between gene_ids and protein_ids (though it would 
> be suboptimal)
> 
> Any suggestions/comments?
> 
> 

> 
> 
> 
> 
> On Thursday 26 August 2004 11:40 am, Y. Thomas Gan wrote:
> > > -----Original Message-----
> > > From: gus...@li...
> > > [mailto:gus...@li...] On Behalf Of 
> > > Steve Fischer
> > > Sent: Wednesday, August 25, 2004 5:18 PM
> > > To: Jinal Jhaveri
> > > Cc: gus...@li...
> > > Subject: Re: [Gusdev-gusdev] dots.nagene to dots.gene
> > >
> > >
> > > To my knowledge we haven't done this yet.   We are just 
> now starting
> > > the planning phases of how to completely use the central dogma to
> > > captures gene, geneinstances, rnas, etc.   So far we have 
> only been
> > > using it partially.
> > >
> > > Others have opinions?
> >
> > I think it is correct in that GUS does not yet have any plugin that 
> > populate the central dogma gene tables, and that annotators 
> make use 
> > of some of these tables.
> >
> > However in our Allgenes project (see allgenes.org), we have 
> pipelines 
> > to build DoTS transcripts (DTs) from ESTs, and DoTS Genes 
> (DGs) from 
> > DTs by aligning them to the genome. In the latter pipeline, I have 
> > plugins (not part of GUS yet) that does the following:
> > 1) make a DoTS.GeneInstanceCategory entry (I made the very first 
> > non-placeholder entry, so I am pretty sure we have not used 
> this table 
> > much before)
> > 2) make DoTS.GeneInstance entries for each of the DGs created by my 
> > pipeline, and give them the gene_instance_category_id I got above
> > 3) associate each DoTS.GeneInstance with a corresponding 
> DoTS.Gene entry
> > (for us, we already have a prior set of DoTS.Gene entries made by an
> > orthogonal algorithm
> > so I only had to map my gene instances to them instead of creating
> > DoTS.Gene entries anew)
> >
> > I also created full sets of DoTS.GeneFeature, DoTS.RnaFeature, 
> > DoTS.ExonFeature, but I will ommit the details here since 
> it is pretty 
> > clear to see from the wiki page how to do this.
> >
> > -Thomas
> >
> > > steve
> > >
> > > On Aug 25, 2004, at 5:47 PM, Jinal Jhaveri wrote:
> > > > Hi,
> > > >
> > > > As per my understanding the "gbparser" loads the uniq genes 
> > > > obtained from the genbank file in dots.nagene table. 
> Our group is 
> > > > planning to do annotation
> > > > (and reannotation) of several genomes and thus we might
> > >
> > > have multiple
> > >
> > > > instances of the same gene and the reviewers might add
> > >
> > > comments etc.
> > >
> > > > All
> > > > these required information is not available with
> > >
> > > dots.nagene but with
> > >
> > > > dots.gene (which make sense). I do understand the handling
> > >
> > > of central
> > >
> > > > dogma
> > > > (thanks to the excellent explanation on WIKI) but what I don't 
> > > > understand is how to handle the transition between each 
> phase. How 
> > > > shall one load the genes
> > > > obtained from the genbank file (i.e in dots.nagene) in 
> dots.gene (&
> > > > dots.geninstance). Is it the matter of writing our own
> > >
> > > script/plugin
> > >
> > > > (I am
> > > > fine with it), or am I missing a very basic step of the
> > >
> > > pipeline? I am
> > >
> > > > asking
> > > > this because, in our project we are at a stage where I have to 
> > > > make decision (which might be very inefficient/wrong from the 
> > > > design
> > >
> > > perspective but
> > >
> > > > FAST
> > > > as far as time is concerned) ,whether to change the GUS
> > >
> > > Schema and let
> > >
> > > > the
> > > > data be in dots.nafeatureimp and dots.nagene table OR 
> to use the 
> > > > dots.gene, dots.geneinstance, etc tables and proceed logically.
> > > >
> > > > Please Help!!!!!!
> > > >
> > > >
> > > > On the other note, I remember Steve mentioning about plans
> > >
> > > to arrange
> > >
> > > > a GUS
> > > > Users Meeting in PCBI, in one of the mails. IMHO It would
> > >
> > > be great if
> > >
> > > > we can
> > > > have that as I know atleast of 3 to 4 more groups (at Virginia 
> > > > Bioinformatics
> > > > Institute)  are planning to use GUS and everyone is waiting
> > >
> > > for a GUS
> > >
> > > > User
> > > > Meeting like this where we can clear our doubts and become more 
> > > > efficient to handle it for our projects. I am sure other groups 
> > > > too will be interested in
> > > > joining this. Any thoughts/comments on the plan ?
> > > >
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > SF.Net email is sponsored by Shop4tech.com-Lowest price on
> > >
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> > > > _______________________________________________
> > > > Gusdev-gusdev mailing list Gus...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> > > -------------------------------------------------------
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> > > _______________________________________________
> > > Gusdev-gusdev mailing list Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> > -------------------------------------------------------
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> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 
> 
> -------------------------------------------------------
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> 

Re: [Gusdev-gusdev] dots.nagene to dots.gene

[Jinal J. <jjh...@vb...>]

Thanks Thomas,

You reply was really helpful. I was thinking on the same track. Here is what I 
am planning to do. I already have one of my genomes annotated (and submited 
to genbank. And I was thinking of generating gbk files for the other genomes 
and submit it to gus using gbparser). So following are the steps I am 
planning to take

1) Parse the genbank file and thus I will have most of my na tables filled
2) Fill the geneinstance and the gene tables and connect geneinstance to 
nafeatureimp using na_feature_id
3) Fill the aa_featureimp table and connect it to nafeatureimp using 
na_feature_id
4) Fill the RNA table(just ids) and connecting it to gene table 
5) Fill the protein_instance table connect it to aafeatureimp through 
aa_feature_id table
6) Fill the protein table and establish relation with RNA using rna_id and  
ofcourse with protein_instance

One thing which isn't clear is how will I fill in the rnainstance table. How 
can this information be available from ncbi genbank? Well I understand that I 
can ignore it for a while and just generate fake rna_ids just to establish 
connection between gene_ids and protein_ids (though it would be suboptimal)

Any suggestions/comments?






On Thursday 26 August 2004 11:40 am, Y. Thomas Gan wrote:
> > -----Original Message-----
> > From: gus...@li...
> > [mailto:gus...@li...] On Behalf
> > Of Steve Fischer
> > Sent: Wednesday, August 25, 2004 5:18 PM
> > To: Jinal Jhaveri
> > Cc: gus...@li...
> > Subject: Re: [Gusdev-gusdev] dots.nagene to dots.gene
> >
> >
> > To my knowledge we haven't done this yet.   We are just now starting
> > the planning phases of how to completely use the central dogma to
> > captures gene, geneinstances, rnas, etc.   So far we have only been
> > using it partially.
> >
> > Others have opinions?
>
> I think it is correct in that GUS does not yet have any plugin
> that populate the central dogma gene tables, and that annotators
> make use of some of these tables.
>
> However in our Allgenes project (see allgenes.org), we have pipelines
> to build DoTS transcripts (DTs) from ESTs, and DoTS Genes (DGs) from DTs
> by aligning them to the genome. In the latter pipeline, I have plugins
> (not part of GUS yet) that does the following:
> 1) make a DoTS.GeneInstanceCategory entry (I made the very first
> non-placeholder entry,
> so I am pretty sure we have not used this table much before)
> 2) make DoTS.GeneInstance entries for each of the DGs created by my
> pipeline,
> and give them the gene_instance_category_id I got above
> 3) associate each DoTS.GeneInstance with a corresponding DoTS.Gene entry
> (for us, we already have a prior set of DoTS.Gene entries made by an
> orthogonal algorithm
> so I only had to map my gene instances to them instead of creating
> DoTS.Gene entries anew)
>
> I also created full sets of DoTS.GeneFeature, DoTS.RnaFeature,
> DoTS.ExonFeature, but I
> will ommit the details here since it is pretty clear to see from the
> wiki page how to do this.
>
> -Thomas
>
> > steve
> >
> > On Aug 25, 2004, at 5:47 PM, Jinal Jhaveri wrote:
> > > Hi,
> > >
> > > As per my understanding the "gbparser" loads the uniq genes obtained
> > > from the
> > > genbank file in dots.nagene table. Our group is planning to do
> > > annotation
> > > (and reannotation) of several genomes and thus we might
> >
> > have multiple
> >
> > > instances of the same gene and the reviewers might add
> >
> > comments etc.
> >
> > > All
> > > these required information is not available with
> >
> > dots.nagene but with
> >
> > > dots.gene (which make sense). I do understand the handling
> >
> > of central
> >
> > > dogma
> > > (thanks to the excellent explanation on WIKI) but what I don't
> > > understand is
> > > how to handle the transition between each phase. How shall one load
> > > the genes
> > > obtained from the genbank file (i.e in dots.nagene) in dots.gene (&
> > > dots.geninstance). Is it the matter of writing our own
> >
> > script/plugin
> >
> > > (I am
> > > fine with it), or am I missing a very basic step of the
> >
> > pipeline? I am
> >
> > > asking
> > > this because, in our project we are at a stage where I have to make
> > > decision
> > > (which might be very inefficient/wrong from the design
> >
> > perspective but
> >
> > > FAST
> > > as far as time is concerned) ,whether to change the GUS
> >
> > Schema and let
> >
> > > the
> > > data be in dots.nafeatureimp and dots.nagene table OR to use the
> > > dots.gene,
> > > dots.geneinstance, etc tables and proceed logically.
> > >
> > > Please Help!!!!!!
> > >
> > >
> > > On the other note, I remember Steve mentioning about plans
> >
> > to arrange
> >
> > > a GUS
> > > Users Meeting in PCBI, in one of the mails. IMHO It would
> >
> > be great if
> >
> > > we can
> > > have that as I know atleast of 3 to 4 more groups (at Virginia
> > > Bioinformatics
> > > Institute)  are planning to use GUS and everyone is waiting
> >
> > for a GUS
> >
> > > User
> > > Meeting like this where we can clear our doubts and become more
> > > efficient to
> > > handle it for our projects. I am sure other groups too will be
> > > interested in
> > > joining this. Any thoughts/comments on the plan ?
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > SF.Net email is sponsored by Shop4tech.com-Lowest price on
> >
> > Blank Media
> >
> > > 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for
> >
> > only $33 Save
> >
> > > 50% off Retail on Ink & Toner - Free Shipping and Free Gift.
> > > http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285
> > > _______________________________________________
> > > Gusdev-gusdev mailing list Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> > -------------------------------------------------------
> > SF.Net email is sponsored by Shop4tech.com-Lowest price on
> > Blank Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic
> > DVD+R for only $33 Save 50% off Retail on Ink & Toner - Free
> > Shipping and Free Gift.
> > http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285
> >
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
> 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33
> Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift.
> http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

RE: [Gusdev-gusdev] dots.nagene to dots.gene

[Y. T. G. <yg...@pc...>]

> -----Original Message-----
> From: gus...@li... 
> [mailto:gus...@li...] On Behalf 
> Of Steve Fischer
> Sent: Wednesday, August 25, 2004 5:18 PM
> To: Jinal Jhaveri
> Cc: gus...@li...
> Subject: Re: [Gusdev-gusdev] dots.nagene to dots.gene
> 
> 
> To my knowledge we haven't done this yet.   We are just now starting 
> the planning phases of how to completely use the central dogma to 
> captures gene, geneinstances, rnas, etc.   So far we have only been 
> using it partially.
> 
> Others have opinions?


I think it is correct in that GUS does not yet have any plugin
that populate the central dogma gene tables, and that annotators 
make use of some of these tables.

However in our Allgenes project (see allgenes.org), we have pipelines
to build DoTS transcripts (DTs) from ESTs, and DoTS Genes (DGs) from DTs
by aligning them to the genome. In the latter pipeline, I have plugins
(not part of GUS yet) that does the following:
1) make a DoTS.GeneInstanceCategory entry (I made the very first
non-placeholder entry,
so I am pretty sure we have not used this table much before)
2) make DoTS.GeneInstance entries for each of the DGs created by my
pipeline,
and give them the gene_instance_category_id I got above
3) associate each DoTS.GeneInstance with a corresponding DoTS.Gene entry
(for us, we already have a prior set of DoTS.Gene entries made by an
orthogonal algorithm
so I only had to map my gene instances to them instead of creating
DoTS.Gene entries anew)

I also created full sets of DoTS.GeneFeature, DoTS.RnaFeature,
DoTS.ExonFeature, but I 
will ommit the details here since it is pretty clear to see from the
wiki page how to do this.

-Thomas

> 
> steve
> 
> 
> On Aug 25, 2004, at 5:47 PM, Jinal Jhaveri wrote:
> 
> > Hi,
> >
> > As per my understanding the "gbparser" loads the uniq genes obtained
> > from the
> > genbank file in dots.nagene table. Our group is planning to do 
> > annotation
> > (and reannotation) of several genomes and thus we might 
> have multiple
> > instances of the same gene and the reviewers might add 
> comments etc. 
> > All
> > these required information is not available with 
> dots.nagene but with
> > dots.gene (which make sense). I do understand the handling 
> of central 
> > dogma
> > (thanks to the excellent explanation on WIKI) but what I don't 
> > understand is
> > how to handle the transition between each phase. How shall one load 
> > the genes
> > obtained from the genbank file (i.e in dots.nagene) in dots.gene (&
> > dots.geninstance). Is it the matter of writing our own 
> script/plugin 
> > (I am
> > fine with it), or am I missing a very basic step of the 
> pipeline? I am 
> > asking
> > this because, in our project we are at a stage where I have to make 
> > decision
> > (which might be very inefficient/wrong from the design 
> perspective but 
> > FAST
> > as far as time is concerned) ,whether to change the GUS 
> Schema and let 
> > the
> > data be in dots.nafeatureimp and dots.nagene table OR to use the 
> > dots.gene,
> > dots.geneinstance, etc tables and proceed logically.
> >
> > Please Help!!!!!!
> >
> >
> > On the other note, I remember Steve mentioning about plans 
> to arrange
> > a GUS
> > Users Meeting in PCBI, in one of the mails. IMHO It would 
> be great if 
> > we can
> > have that as I know atleast of 3 to 4 more groups (at Virginia 
> > Bioinformatics
> > Institute)  are planning to use GUS and everyone is waiting 
> for a GUS 
> > User
> > Meeting like this where we can clear our doubts and become more 
> > efficient to
> > handle it for our projects. I am sure other groups too will be 
> > interested in
> > joining this. Any thoughts/comments on the plan ?
> >
> >
> >
> > -------------------------------------------------------
> > SF.Net email is sponsored by Shop4tech.com-Lowest price on 
> Blank Media 
> > 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for 
> only $33 Save 
> > 50% off Retail on Ink & Toner - Free Shipping and Free Gift. 
> > http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285
> > _______________________________________________
> > Gusdev-gusdev mailing list Gus...@li...
> > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> 
> 
> 
> -------------------------------------------------------
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> 

Re: [Gusdev-gusdev] dots.nagene to dots.gene

[Steve F. <sfi...@pc...>]

To my knowledge we haven't done this yet.   We are just now starting 
the planning phases of how to completely use the central dogma to 
captures gene, geneinstances, rnas, etc.   So far we have only been 
using it partially.

Others have opinions?

steve


On Aug 25, 2004, at 5:47 PM, Jinal Jhaveri wrote:

> Hi,
>
> As per my understanding the "gbparser" loads the uniq genes obtained 
> from the
> genbank file in dots.nagene table. Our group is planning to do 
> annotation
> (and reannotation) of several genomes and thus we might have multiple
> instances of the same gene and the reviewers might add comments etc. 
> All
> these required information is not available with dots.nagene but with
> dots.gene (which make sense). I do understand the handling of central 
> dogma
> (thanks to the excellent explanation on WIKI) but what I don't 
> understand is
> how to handle the transition between each phase. How shall one load 
> the genes
> obtained from the genbank file (i.e in dots.nagene) in dots.gene (&
> dots.geninstance). Is it the matter of writing our own script/plugin 
> (I am
> fine with it), or am I missing a very basic step of the pipeline? I am 
> asking
> this because, in our project we are at a stage where I have to make 
> decision
> (which might be very inefficient/wrong from the design perspective but 
> FAST
> as far as time is concerned) ,whether to change the GUS Schema and let 
> the
> data be in dots.nafeatureimp and dots.nagene table OR to use the 
> dots.gene,
> dots.geneinstance, etc tables and proceed logically.
>
> Please Help!!!!!!
>
>
> On the other note, I remember Steve mentioning about plans to arrange 
> a GUS
> Users Meeting in PCBI, in one of the mails. IMHO It would be great if 
> we can
> have that as I know atleast of 3 to 4 more groups (at Virginia 
> Bioinformatics
> Institute)  are planning to use GUS and everyone is waiting for a GUS 
> User
> Meeting like this where we can clear our doubts and become more 
> efficient to
> handle it for our projects. I am sure other groups too will be 
> interested in
> joining this. Any thoughts/comments on the plan ?
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
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[Gusdev-gusdev] dots.nagene to dots.gene

[Jinal J. <jjh...@vb...>]

Hi, 

As per my understanding the "gbparser" loads the uniq genes obtained from the 
genbank file in dots.nagene table. Our group is planning to do annotation 
(and reannotation) of several genomes and thus we might have multiple 
instances of the same gene and the reviewers might add comments etc. All 
these required information is not available with dots.nagene but with 
dots.gene (which make sense). I do understand the handling of central dogma 
(thanks to the excellent explanation on WIKI) but what I don't understand is 
how to handle the transition between each phase. How shall one load the genes 
obtained from the genbank file (i.e in dots.nagene) in dots.gene (& 
dots.geninstance). Is it the matter of writing our own script/plugin (I am 
fine with it), or am I missing a very basic step of the pipeline? I am asking 
this because, in our project we are at a stage where I have to make decision 
(which might be very inefficient/wrong from the design perspective but FAST 
as far as time is concerned) ,whether to change the GUS Schema and let the 
data be in dots.nafeatureimp and dots.nagene table OR to use the dots.gene, 
dots.geneinstance, etc tables and proceed logically. 

Please Help!!!!!!


On the other note, I remember Steve mentioning about plans to arrange a GUS 
Users Meeting in PCBI, in one of the mails. IMHO It would be great if we can 
have that as I know atleast of 3 to 4 more groups (at Virginia Bioinformatics 
Institute)  are planning to use GUS and everyone is waiting for a GUS User 
Meeting like this where we can clear our doubts and become more efficient to 
handle it for our projects. I am sure other groups too will be interested in 
joining this. Any thoughts/comments on the plan ?

Re: [Gusdev-gusdev] Go annotation upload

[Steve F. <sfi...@pc...>]

see below  -steve

On Aug 25, 2004, at 2:56 PM, Dave Barkan wrote:

> Correct, sorry about that.  I bet it would not take too much to make 
> an equivalent plugin that loads NA sequences, however.  You could 
> probably copy a lot of the code from LoadGoAssociation.pm to 
> accomplish this, and almost certainly retain the CBIL::Bio parsing 
> modules.
>

please *don't* copy code.  instead, factor the common code into a 
shareable module.

steve

> Dave
>
> On Wed, 25 Aug 2004, Thomas Otto wrote:
>
>> Hi Dave,
>>
>> I went back to the subject to upload the go-annotations. Sadly it 
>> just works with AA sequences, - I have the impression the 
>> documentation is far better now.
>> Is there someone how already did a plugin to assoziate also NA 
>> sequences to the go annotations of 
>> http://www.geneontology.org/GO.current.annotations.shtml?
>>
>> Cheers,
>> Thomas
>>
>>>>>> Hello -,
>>>>>> with witch plugin can I upload the Goannotations from the 
>>>>>> http://www.geneontology.org/GO.current.annotations.shtml page?
>>>>>> Thanks in advance,
>>>>>> Thomas
>>>>>> -------------------------------------------------------
>>>>>> This SF.Net email is sponsored by BEA Weblogic Workshop
>>>>>> FREE Java Enterprise J2EE developer tools!
>>>>>> Get your free copy of BEA WebLogic Workshop 8.1 today.
>>>>>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>>>>>> _______________________________________________
>>>>>> Gusdev-gusdev mailing list
>>>>>> Gus...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>> -------------------------------------------------------
>>>>> This SF.Net email is sponsored by BEA Weblogic Workshop
>>>>> FREE Java Enterprise J2EE developer tools!
>>>>> Get your free copy of BEA WebLogic Workshop 8.1 today.
>>>>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>>
>> -------------------------------------------------------
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>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
> -------------------------------------------------------
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> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] Go annotation upload

[Dave B. <db...@pc...>]

Correct, sorry about that.  I bet it would not take too much to make an 
equivalent plugin that loads NA sequences, however.  You could probably 
copy a lot of the code from LoadGoAssociation.pm to accomplish this, and 
almost certainly retain the CBIL::Bio parsing modules.

Dave

On Wed, 25 Aug 2004, Thomas Otto wrote:

> Hi Dave,
>
> I went back to the subject to upload the go-annotations. Sadly it just works 
> with AA sequences, - I have the impression the documentation is far better 
> now.
> Is there someone how already did a plugin to assoziate also NA sequences to 
> the go annotations of 
> http://www.geneontology.org/GO.current.annotations.shtml?
>
> Cheers,
> Thomas
>
>>>>> Hello -,
>>>>> 
>>>>> with witch plugin can I upload the Goannotations from the 
>>>>> http://www.geneontology.org/GO.current.annotations.shtml page?
>>>>> 
>>>>> Thanks in advance,
>>>>> 
>>>>> Thomas
>>>>> 
>>>>> 
>>>>> -------------------------------------------------------
>>>>> This SF.Net email is sponsored by BEA Weblogic Workshop
>>>>> FREE Java Enterprise J2EE developer tools!
>>>>> Get your free copy of BEA WebLogic Workshop 8.1 today.
>>>>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>>>>> _______________________________________________
>>>>> Gusdev-gusdev mailing list
>>>>> Gus...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>> 
>>>> 
>>>> 
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by BEA Weblogic Workshop
>>>> FREE Java Enterprise J2EE developer tools!
>>>> Get your free copy of BEA WebLogic Workshop 8.1 today.
>>>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>> 
>>> 
>> 
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
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> Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift.
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> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] Problem with GBParser plugin

[Jeetendra S. <so...@vb...>]

Hi all,

I tried to look for a solution to this problem in the archive, but
couldn't find one.
When I tried to upload a certain Genbank flat file using GBParser plugin,
it never terminated. After degugging I figured out that when there are no
trailing spaces after ORIGIN, the plugin never terminates. That is, it
works okay when there are spaces after ORIGIN, otherwise not.

Any solution to this ?

Thank you,
Jeetendra.

Re: [Gusdev-gusdev] Error in GUS application?

[Steve F. <sfi...@pc...>]

Not a very good error message...

I think the problem is a missing colon in your command line.  You have  
"ga +update GUS:Common"

steve

On Aug 25, 2004, at 12:04 PM, Ed Robinson wrote:

> Does anyone recognize this?  It has Pablo and I stumped.  Hopefully,  
> it is something simple like updating CVS.
>
> ---------------------------
> [erobinso@mkiwi PluginMgr]$ ga +update  
> GUS:Common::Plugin::LoadNASequenceFromTigrXML --commit
>
> ERROR: syntax error at (eval 3) line 1, near "require GUS:"
>
>
> --------------------------- STACK TRACE -------------------------
>          
> GUS::PluginMgr::Plugin::error('GUS::PluginMgr:: 
> GusApplication=HASH(0x80fbb4c)', 'syntax error at (eval 3) line 1,  
> near "require GUS:"^J') called at  
> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 248
>          
> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr:: 
> GusApplication=HASH(0x80fbb4c)',  
> 'GUS:Common::Plugin::LoadNASequenceFromTigrXML') called at  
> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 664
>          
> GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS:: 
> PluginMgr::GusApplication=HASH(0x80fbb4c)', 1,  
> 'GUS:Common::Plugin::LoadNASequenceFromTigrXML') called at  
> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 466
>          
> GUS::PluginMgr::GusApplication::doMajorMode_Update('GUS::PluginMgr:: 
> GusApplication=HASH(0x80fbb4c)',  
> 'GUS:Common::Plugin::LoadNASequenceFromTigrXML') called at  
> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
>          
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr:: 
> GusApplication=HASH(0x80fbb4c)',  
> 'GUS:Common::Plugin::LoadNASequenceFromTigrXML') called at  
> /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
>          
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr:: 
> GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at  
> /var/local/gus_home/bin/ga line 11
>
>
> -Ed Robinson
> Project Specialist
> CTEGD, Univeristy of Georgia
> Athens, GA 30601
>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
> 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33
> Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift.
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> _______________________________________________
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> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [Gusdev-gusdev] Error in GUS application?

[Angel P. <an...@pc...>]

Looks like some funny character encoding in the file within an eval 
statement. Maybe some non-unix new line between the "::" in "GUS::Model..."
Angel
Ed Robinson wrote:

>Does anyone recognize this?  It has Pablo and I stumped.  Hopefully, it is something simple like updating CVS.
>
>---------------------------
>[erobinso@mkiwi PluginMgr]$ ga +update GUS:Common::Plugin::LoadNASequenceFromTigrXML --commit
> 
>ERROR: syntax error at (eval 3) line 1, near "require GUS:"
> 
>  
>

[Gusdev-gusdev] Error in GUS application?

[Ed R. <ed_...@be...>]

Does anyone recognize this?  It has Pablo and I stumped.  Hopefully, it is something simple like updating CVS.

---------------------------
[erobinso@mkiwi PluginMgr]$ ga +update GUS:Common::Plugin::LoadNASequenceFromTigrXML --commit
 
ERROR: syntax error at (eval 3) line 1, near "require GUS:"
 
 
--------------------------- STACK TRACE -------------------------
        GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'syntax error at (eval 3) line 1, near "require GUS:"^J') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 248
        GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS:Common::Plugin::LoadNASequenceFromTigrXML') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 664
        GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 1, 'GUS:Common::Plugin::LoadNASequenceFromTigrXML') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 466
        GUS::PluginMgr::GusApplication::doMajorMode_Update('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS:Common::Plugin::LoadNASequenceFromTigrXML') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 283
        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'GUS:Common::Plugin::LoadNASequenceFromTigrXML') called at /var/local/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 192
        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb4c)', 'ARRAY(0x8102dbc)') called at /var/local/gus_home/bin/ga line 11


-Ed Robinson
Project Specialist
CTEGD, Univeristy of Georgia
Athens, GA 30601

Re: [Gusdev-gusdev] Go annotation upload

[Thomas O. <ot...@fi...>]

Hi Dave,

I went back to the subject to upload the go-annotations. Sadly it just 
works with AA sequences, - I have the impression the documentation is 
far better now.
Is there someone how already did a plugin to assoziate also NA sequences 
to the go annotations of 
http://www.geneontology.org/GO.current.annotations.shtml?

Cheers,
Thomas

>>>> Hello -,
>>>>
>>>> with witch plugin can I upload the Goannotations from the 
>>>> http://www.geneontology.org/GO.current.annotations.shtml page?
>>>>
>>>> Thanks in advance,
>>>>
>>>> Thomas
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by BEA Weblogic Workshop
>>>> FREE Java Enterprise J2EE developer tools!
>>>> Get your free copy of BEA WebLogic Workshop 8.1 today.
>>>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>>>> _______________________________________________
>>>> Gusdev-gusdev mailing list
>>>> Gus...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by BEA Weblogic Workshop
>>> FREE Java Enterprise J2EE developer tools!
>>> Get your free copy of BEA WebLogic Workshop 8.1 today.
>>> http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>
>

Re: [Gusdev-gusdev] updating with GBParser

[Angel P. <an...@pc...>]

Jeetendra Soneja wrote:

>Hi all,
>When the GBParser plugin figures out that the sequence with the accession
>number is already present, it tries to update it.
>Now, what are the exact updates that take place ? If the number of
>features have changed, does it add/delete the features to the already
>existing sequence in the database ? Does it make the changes to actual
>sequence ?
>
>I would appreciate if someone could provide me this information.
>
>Thanks,
>Jeetendra.
>
>
>  
>
If the sequence  changed it updates the sequence

It treats features as follows:
It retrieves all of the existing record's features.
It builds a NEW records with all the features from the gbff record
It does a graph-based comparison to find matches for features of both 
object graphs
Any feature from the existing record that is not matched to the new 
record should be deleted
Any feature in the new record that is not matched to the existing 
records are added to the new record
The existing record is then committed.

In essence, I don't do an "update" but rather a delete then re-insert 
for changed features.

Angel

[Gusdev-gusdev] updating with GBParser

[Jeetendra S. <so...@vb...>]

Hi all,
When the GBParser plugin figures out that the sequence with the accession
number is already present, it tries to update it.
Now, what are the exact updates that take place ? If the number of
features have changed, does it add/delete the features to the already
existing sequence in the database ? Does it make the changes to actual
sequence ?

I would appreciate if someone could provide me this information.

Thanks,
Jeetendra.


-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu

[Gusdev-gusdev] problems with gus installation

[Dominik L. B. <do...@vb...>]

Hello,
I'm attempting to install GUS, and each time I run the build it gets to the 
following point, upon which it simply never finishes:

     [exec] generating perl object for DoTS::AAEntry
     [exec] generating perl object for DoTS::AAFamilyExperiment
     [exec] generating perl object for DoTS::AAFeature

Is there a way to set the build process to produce more verbose output? 
Changing ant invocation in build.pl to -v does add some more details, but not 
for those steps. What exactly is performed during the generating of perl 
objects?

Any hints/suggestions would be greatly welcomed.

Sincerely,
dom

Re: [Gusdev-gusdev] how can I download GUS Schema 3.0?

[sammy <gus...@ya...>]

Dear Jeetendra Soneja,

thank you very much for your help! I have downloaded
it according to the instruction on the Sanger website.

Thanks again,
Sammy


--- Jeetendra Soneja <so...@vb...> wrote:

> The CVS command should work on linux-like systems. I
> downloaded the GUS
> schema only last week. It worked fine. I followed in
> the instructions on
> the Sanger website.
> 
> If it still doesn't work, could you send the actual
> command that you are
> giving and the error message that you are getting.
> 
> --Jeetendra.
> 
> 
> > Dear friends,
> >
> > sorry to ask a newbie question, could you please
> tell
> > me how can I download GUS Schema 3.0?
> >
> > I tried cvs command and didn't work, then
> according to
> > the instruction of "Public CVS Repository", I
> can't
> > find the link that says "Download this directory
> in
> > tarball".
> >
> > it seems weird, could someone help me to solve
> this
> > problem if you happen to know the answer?
> >
> > Thank you very much for your help!
> > Sammy
> >
> >
> >
> > __________________________________
> > Do you Yahoo!?
> > New and Improved Yahoo! Mail - Send 10MB messages!
> > http://promotions.yahoo.com/new_mail
> >
> >
> >
>
-------------------------------------------------------
> > SF.Net email is sponsored by Shop4tech.com-Lowest
> price on Blank Media
> > 100pk Sonic DVD-R 4x for only $29 -100pk Sonic
> DVD+R for only $33
> > Save 50% off Retail on Ink & Toner - Free Shipping
> and Free Gift.
> >
>
http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285
> > _______________________________________________
> > Gusdev-gusdev mailing list
> > Gus...@li...
> >
>
https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >
> 
> 
> -- 
> Jeetendra Soneja
> Research Associate
> Virginia Bioinformatics Institute
> 1880 Pratt Dr., Building XV
> Blacksburg, VA 24060, USA
> Phone: (540)-231-2789
> http://www.vbi.vt.edu
> 



		
__________________________________
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[Gusdev-gusdev] how can I download GUS Schema 3.0?

[sammy <gus...@ya...>]

Dear friends,

sorry to ask a newbie question, could you please tell
me how can I download GUS Schema 3.0?

I tried cvs command and didn't work, then according to
the instruction of "Public CVS Repository", I can't
find the link that says "Download this directory in
tarball".

it seems weird, could someone help me to solve this
problem if you happen to know the answer?

Thank you very much for your help!
Sammy


		
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Re: [Gusdev-gusdev] Homology Data - loading process into GUS

[Pablo N. M. <pa...@pa...>]

Hi Arnaud,
I'm working on orthologous analyses as described in:
http://www.egg.isu.edu/biocourses/bios692/orthomcl

The scripts were provided by Li Li (li...@pc...).

Cheers,
Pablo

On Thu, 2004-08-19 at 07:13, Arnaud Kerhornou wrote: 
> Hi
> 
> I would like to know if there is anything already implemented to process 
> homology data (gene clusters and orthologues data).
> 
> Re. Orthologoues data, we use reciprocal blastp wrapper to generate the 
> orthologous groups, giving a set of cutoff parameters.
> 
> Re. clustering genes within a species into families, we blast a proteome 
> against itself and then run tribe to generate a set of clusters and 
> their members.
> 
> Has anyone worked on processing such data for loading into GUS3 ?
> 
> Thanks
> Arnaud
> 


-- 
-----------------------------
Pablo Nascimento Mendes
CTEGD EMF TIPS Fellow
Kissinger Lab
Department of Genetics
University of Georgia
C210 Life Sciences Bldg.
Athens, Georgia 30602
Phone:706 542-1447
E-mail: pa...@ug...

Re: [Gusdev-gusdev] GBParser error

[Deborah F. P. <pi...@pc...>]

Hi Jeetendra,

In a sense the taxon:xxxxx is linked to the sres.taxon and sres.taxonname 
tables but through the SOURCE line. The xxxxx is the NCBI tax_id which is 
is an attribute in the taxon table (ncbi_tax_id). The GBParser uses the 
genus species name on the SOURCE line to retrieve the sres.taxon.taxon_id 
by executing a query that does a join between taxonname and taxon. 
Obviously it is better if taxon and taxonname are up to date.

The reason that it is done this way is that all GenBank records have a 
Source line but many do not have a db_xref="taxon:xxxx".

                                                     Debbie


On Thu, 19 Aug 2004, Jeetendra Soneja wrote:

> Dear Steve,
>
> Thank you for your reply. You were right, I accidently pasted incomplete
> error message.
>    As you and Pablo suggested, I took a look at the sequence value for
> the ExternalDatabase table, and it was set to '1'. I altered the
> sequence and set its value to the number of records in
> ExternalDatabase table. It's working fine now.
>    Some thoughts on how this problem might have occured. As suggested in
> the GUS documentation, I populated the Sres.ExternalDatabase and
> Sres.ExternalDatabaseRelease tables using the SubmitRow plugin. I
> suppose that SubmitRow doesn't use the sequence value associated with
> these tables, and hence they retain their initial value (equal to 1).
> This can cause conflict as it did in my case. Is that correct ?
>    Also, it would be nice if we could link the 'db_xref="taxon:xxxx"'
> qualifier of Genbank file to Sres.Taxon and Sres.TaxonName tables.
>
> Regards,
> Jeetendra.
>
>
>> dear Jeetendra -
>>
>> it looks like the genbank parser does force a new external database
>> called taxon into the ExternalDatabase table, as it doesn't seem to have
>> a facility to map 'taxon' to an alternative name for that db.
>>
>> it looks like its failing because it may be having trouble with the
>> sequence (db sequence, not bio sequence) which generates the next key.
>>
>> did you send the complete error output?   I am not sure i understand why
>> i am not seeing a primary key value in the insert statement.
>>
>> steve
>>
>>
>> Jeetendra Soneja wrote:
>>
>>> I am trying to upload a genbank flat file, and I am getting the error
>>> listed below.
>>>    When I looked at the source code of GbParser.pm, I figured out that
>>> the plugin is getting the database name as 'taxon' from the db_xref
>>> qualifier (e.g. db_xref='taxon:4932') and is trying to retrieve the
>>> external_database_id and external_database_release_id for the 'taxon'
>>> database. Now, even though I have an entry for 'Taxonomy' database in
>>> my Sres.ExternalDatabase table, it is unable to match that since it is
>>> looking for 'taxon' as the database name. Finally, it tries to insert
>>> new entry for 'taxon' database in the Sres.ExternalDatabase and
>>> Sres.ExternalDatabaseRelease tables, and the insert statement fails ..
>>> don't know why ?
>>>
>>> I would greatly appreciate if someone could help me on this.
>>>
>>> Thanks,
>>> Jeetendra.
>>>
>>>
>>>
>>> allNonNullsSet: db_ref_na_feature_id not set... = ''
>>> allNonNullsSet: external_database_id not set... = ''
>>> GUS::Model::SRes::ExternalDatabase->retrieveFromDB($doNotRetrieveAtts=,)
>>> Submitting GUS::Model::SRes::ExternalDatabase:
>>> Table: ExternalDatabase
>>>        lowercase_name: [taxon]
>>>        name: [taxon]
>>>
>>> HasChangedAttributes='0'
>>> Setting all foreign keys
>>> GUS::Model::SRes::ExternalDatabase->Submit: All foreign keys are
>>> set...proceeding
>>> allNonNullsSet: external_database_id not set... = ''
>>> Inserting:
>>> Table: ExternalDatabase
>>>        group_write: [1]
>>>        other_read: [1]
>>>        group_read: [1]
>>>        lowercase_name: [taxon]
>>>        name: [taxon]
>>>        user_read: [1]
>>>        row_user_id: [1]
>>>        modification_date: [SYSDATE]
>>>        other_write: [0]
>>>        row_alg_invocation_id: [171]
>>>        row_project_id: [1]
>>>        row_group_id: [1]
>>>        user_write: [1]
>>> DBD::Oracle::st execute failed: ORA-00001: unique constraint
>>> (SRES.PK_EXTERNALDATABASE) violated (DBD ERROR: OCIStmtExecute)$
>>>    INSERT INTO SRes.ExternalDatabase (  group_write, other_read,
>>> group_read, lowercase_name, name, user_read, row_user_id, $
>>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with
>>> ParamValues: :p5='taxon', :p12='1', :p8='7', :p10='1$
>>> Wed Aug 18 17:44:50 2004        Genbank entries inserted= 0;  updated= 0;
>>> total #(inserted::updated::deleted)=16::::
>>>
>>> Wed Aug 18 17:44:50 2004        FAILURES        Unable to process 2
>>> entries. See gbparserFailures/
>>> Wed Aug 18 17:44:50 2004        RESULT  Genbank entries inserted= 0;
>>> updated= 0;  failed= 2
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
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>
>
> --
> Jeetendra Soneja
> Research Associate
> Virginia Bioinformatics Institute
> 1880 Pratt Dr., Building XV
> Blacksburg, VA 24060, USA
> Phone: (540)-231-2789
> http://www.vbi.vt.edu
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
> 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33
> Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift.
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> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

[Gusdev-gusdev] Homology Data - loading process into GUS

[Arnaud K. <ax...@sa...>]

Hi

I would like to know if there is anything already implemented to process 
homology data (gene clusters and orthologues data).

Re. Orthologoues data, we use reciprocal blastp wrapper to generate the 
orthologous groups, giving a set of cutoff parameters.

Re. clustering genes within a species into families, we blast a proteome 
against itself and then run tribe to generate a set of clusters and 
their members.

Has anyone worked on processing such data for loading into GUS3 ?

Thanks
Arnaud

Re: [Gusdev-gusdev] GBParser error

[Jeetendra S. <so...@vb...>]

Dear Steve,

Thank you for your reply. You were right, I accidently pasted incomplete
error message.
    As you and Pablo suggested, I took a look at the sequence value for
the ExternalDatabase table, and it was set to '1'. I altered the
sequence and set its value to the number of records in
ExternalDatabase table. It's working fine now.
    Some thoughts on how this problem might have occured. As suggested in
the GUS documentation, I populated the Sres.ExternalDatabase and
Sres.ExternalDatabaseRelease tables using the SubmitRow plugin. I
suppose that SubmitRow doesn't use the sequence value associated with
these tables, and hence they retain their initial value (equal to 1).
This can cause conflict as it did in my case. Is that correct ?
    Also, it would be nice if we could link the 'db_xref="taxon:xxxx"'
qualifier of Genbank file to Sres.Taxon and Sres.TaxonName tables.

Regards,
Jeetendra.


> dear Jeetendra -
>
> it looks like the genbank parser does force a new external database
> called taxon into the ExternalDatabase table, as it doesn't seem to have
> a facility to map 'taxon' to an alternative name for that db.
>
> it looks like its failing because it may be having trouble with the
> sequence (db sequence, not bio sequence) which generates the next key.
>
> did you send the complete error output?   I am not sure i understand why
> i am not seeing a primary key value in the insert statement.
>
> steve
>
>
> Jeetendra Soneja wrote:
>
>>I am trying to upload a genbank flat file, and I am getting the error
>>listed below.
>>    When I looked at the source code of GbParser.pm, I figured out that
>>the plugin is getting the database name as 'taxon' from the db_xref
>>qualifier (e.g. db_xref='taxon:4932') and is trying to retrieve the
>>external_database_id and external_database_release_id for the 'taxon'
>>database. Now, even though I have an entry for 'Taxonomy' database in
>>my Sres.ExternalDatabase table, it is unable to match that since it is
>>looking for 'taxon' as the database name. Finally, it tries to insert
>>new entry for 'taxon' database in the Sres.ExternalDatabase and
>>Sres.ExternalDatabaseRelease tables, and the insert statement fails ..
>>don't know why ?
>>
>>I would greatly appreciate if someone could help me on this.
>>
>>Thanks,
>>Jeetendra.
>>
>>
>>
>>allNonNullsSet: db_ref_na_feature_id not set... = ''
>>allNonNullsSet: external_database_id not set... = ''
>>GUS::Model::SRes::ExternalDatabase->retrieveFromDB($doNotRetrieveAtts=,)
>>Submitting GUS::Model::SRes::ExternalDatabase:
>> Table: ExternalDatabase
>>        lowercase_name: [taxon]
>>        name: [taxon]
>>
>>HasChangedAttributes='0'
>>Setting all foreign keys
>>GUS::Model::SRes::ExternalDatabase->Submit: All foreign keys are
>>set...proceeding
>>allNonNullsSet: external_database_id not set... = ''
>>Inserting:
>>Table: ExternalDatabase
>>        group_write: [1]
>>        other_read: [1]
>>        group_read: [1]
>>        lowercase_name: [taxon]
>>        name: [taxon]
>>        user_read: [1]
>>        row_user_id: [1]
>>        modification_date: [SYSDATE]
>>        other_write: [0]
>>        row_alg_invocation_id: [171]
>>        row_project_id: [1]
>>        row_group_id: [1]
>>        user_write: [1]
>>DBD::Oracle::st execute failed: ORA-00001: unique constraint
>>(SRES.PK_EXTERNALDATABASE) violated (DBD ERROR: OCIStmtExecute)$
>>    INSERT INTO SRes.ExternalDatabase (  group_write, other_read,
>>group_read, lowercase_name, name, user_read, row_user_id, $
>>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? ) " with
>>ParamValues: :p5='taxon', :p12='1', :p8='7', :p10='1$
>>Wed Aug 18 17:44:50 2004        Genbank entries inserted= 0;  updated= 0;
>>total #(inserted::updated::deleted)=16::::
>>
>>Wed Aug 18 17:44:50 2004        FAILURES        Unable to process 2
>>entries. See gbparserFailures/
>>Wed Aug 18 17:44:50 2004        RESULT  Genbank entries inserted= 0;
>>updated= 0;  failed= 2
>>
>>
>>
>>
>>
>>
>
>
>
> -------------------------------------------------------
> SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media
> 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33
> Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift.
> http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 
Jeetendra Soneja
Research Associate
Virginia Bioinformatics Institute
1880 Pratt Dr., Building XV
Blacksburg, VA 24060, USA
Phone: (540)-231-2789
http://www.vbi.vt.edu