[Biojava-l] Bibliographic objects

[Tom Oinn]

Thomas Down wrote:
> 
> This isn't a new idea
> 
>    (http://biojava.org/pipermail/biojava-l/2000-May/000249.html)
> 
> but...  I'm interested in deverloping a [Bibliographic] reference
> object model in BioJava.  These objects would be constructed
> by things like EmblProcessor (and SwissprotProcessor) from the
> headers of sequence records.  If we get them right, they might
> also have many other applications, including running
> stand-alone reference databases.
> 
> Is there any demand for this?

Yes. We (in this case We -> Interpro programmers) are also thinking
about this, as we have what is tending towards a unified model for
references within EMBL, SWISSPROT and InterPro. We found the following
problems....

1. The databases that we ideally want to be able to model citations in
are not very good from the point of view of consistancy. We find many
mis-spellings, etc.

2. We're looking from the relational database viewpoint mostly, so our
ideas are focused on simple mappings between object and relational
models. This may not sit well with what you're thinking of, but it
may.

3. We're under the usual time constraints (i.e. heads of group saying
things like 'we need our unified reference database as soon as
possible'), which never helps.

Would any of the Sanger people have time to call round to the EBI? I
can attempt to arrange all the interested people at this end, probably
in a few weeks. Suggestions?

Cheers,

Tom


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It's why I chew their heads off,
They're good for breakfast	
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