[Bioperl-l] [BioSQL-l] SwissProt DE lines and bioentry.description field in BioSQL

Peter biopython at maubp.freeserve.co.uk
Sat May 16 19:28:43 EDT 2009

On 5/17/09, Chris Fields <cjfields at illinois.edu> wrote:
> On May 16, 2009, at 5:34 PM, Hilmar Lapp wrote:
> > My inclination from a BioPerl perspective is to extract the part following
> > 'RecName: Full=' as the description, and attach the rest as annotation. We
> > could in fact use the TagTree class for this. I'm cross-posting to BioPerl
> > too to gather what other BioPerl'ers think about this.
> >
> >        -hilmar
> >
> This is much like the GN issues we've run into before, and we *could* set
> this up using TagTree or similar.  In the latter case of gene name the data
> is stored in a text tree as follows:
>  gene_names:
>   gene_name:
>     Name: GC1QBP
>     Synonyms: HABP1
>     Synonyms: SF2P32
>     Synonyms: C1QBP
>  That could be changed to an XML string:
>  <?xml version="1.0" encoding="UTF-8"?>
>  <gene_names>
>   <gene_name>
>     <Name>GC1QBP</Name>
>     <Synonyms>HABP1</Synonyms>
>     <Synonyms>SF2P32</Synonyms>
>     <Synonyms>C1QBP</Synonyms>
>   </gene_name>
>  </gene_names>
> Thinking about this we should attempt to coalesce around a standard instead
> of forcing the other Bio*  to a specific format.

How would you record this in BioSQL?  As an XML string for an annotation value?

Brad has suggested JSON might be useful for this kind of thing (see
also per-letter-annotation discussion).


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