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

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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 ?
> > >
> > >
> > >
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