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

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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 ?
> > > >
> > > >
> > > >
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