Source_Exons tag

Richard Durbin rd at sanger.ac.uk
Tue Oct 30 09:38:13 EST 2001

We have talked for some time about ways to support an alternative exon implementation
for acedb/fmap more in line with what is standard elsewhere, i.e. having separate exon
objects, with transcripts linking to the exons that they contain.  Time to have this
discussion with proposals in the open in the acedb newsgroup, I think.

Should we also support Intron objects?  If so, would either exons or introns be
acceptable, and what happens if both are given and they are inconsistent?

I hasten to add, for reasons of continuity, and because some people strongly like
all the exon structure information being explicit in the transcript-type objects,
I expect we will continue to support the current style.


Tim Cutts wrote:
> Greetings all:
> One of my tasks here is to synchronise genomic data between ACeDB and a
> relational database.
> An issue with this is that ACeDB does not represent exons in transcripts
> as individual objects, but merely as tags within a ?Sequence object.
> However, I would like to be able to store the unique IDs that these
> exons have in the relational database in ACeDB.
> Thus, I am considering adding an extra field to the Source_exons tag in
> ?Sequence to store the exon's id.
> I am concerned though, that this is a part of the model which is tightly
> integrated with the FMAP display (and possibly much else) and
> consequently this could well be a bad idea, in case AceDB's developers
> opt to change the Source_Exon model themselves later.
> Does anyone have any thoughts as to how this could be achieved in such a
> way that it won't break with future releases of ACeDB?
> Thanks,
> Tim.
> --
> "It is the job of Sales and Marketing to insulate those who know what
> they're talking about from each other"
>   -- I know who said this, but I'm not telling.

Richard Durbin                                      The Sanger Centre
email: rd at sanger.ac.uk                   Wellcome Trust Genome Campus
http://www.sanger.ac.uk/Users/rd/                             Hinxton
phone: 01223 494978                                Cambridge CB10 1SA
fax: 01223 494919                                                  UK

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