[Bioperl-l] OMIM parser

[Ewan Birney]

On Thu, 11 Jul 2002, Chris Zmasek wrote:

> Hi!
>
> I am in the process of writing a parser for the OMIM database (to be submitted to Bioperl).
>
> Not all entries in OMIM are linked to a gene/locus, some of them are just diseases without a associated gene, for example the entry for "ABDOMINAL AORTIC ANEURYSM" (100070).
>
> Therefore I am not clear what the best output for such a parser might be:
> Sequence objects (without a actual "sequence string") or annotation objects?
> If the output consists of sequence objects, entries without a associated gene would have to be ignored.
>
> What do you think?

Interesting problem. I think OMIM is essentially a set of Annotation
Collections. The links to sequence I would claim are DBxREF style links,
not Bio::Seq style objects. Would parser being


   $ominio->next_annotationcollection() # hmmm a little long winded


be good?




>
> Thanks,
>
> Christian [czmasek@gnf.org]
>
>
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