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 ?
> >
> >
> >
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