[Biopython-dev] SwissProt DE lines and UniProt XML / TagTree as XML in BioSQL

[Andrea Pierleoni]

I think that the point here can be a little broader, since not only the
swissprot DE lines carry complex and structured data.
To define a common, language-independent way to store structured data into
the comment and *_qualifier_value tables of the actual BioSQL schema could
be very useful.
XML looks like a good candidate to me, and the UniprotXML format can be
used as reference or as a template to start from.
Each Bio* project will then parse and report this structured data in its
own programming language data structure.

Andrea


> Hi all,
>
> This is cross posted to try and ensure relevant people see it.
> I suggest we continue the discussion on the BioSQL list
> (for how to serialise structured annotation to BioSQL), and/or
> the OpenBio list (for things like file format naming conventions).
>
> I am hoping we (Bio*) can be consistent in how we parse and load
> into BioSQL the SwissProt DE lines (known as "swiss" format in
> both BioPerl and Biopython's SeqIO, and by EMBOSS) or the
> equivalent UniProt XML tags (which we are tentatively going to
> call the "uniprot" format in Biopython's SeqIO - comments?).
>
> Like BioPerl (etc), Biopython can parse plain text SwissProt ("swiss")
> files and load them into BioSQL. Biopython currently treats the DE
> comment lines as a long string, as BioPerl used to:
>
> http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030041.html
> http://lists.open-bio.org/pipermail/biosql-l/2009-May/001514.html
>
> I understand that BioPerl now turns the SwissProt DE lines into a
> TagTree, and for storing this in BioSQL this gets serialised as XML.
> I would like Biopython to handle this the same way (although rather
> than a Perl TagTree, we'd use a Python structure of course), and
> would appreciate clarification of what exactly was implemented
> (e.g. which bit of the BioPerl source code should be look at,
> and could you show a worked example?).
>
> Andrea Pierlenoin (CC'd - not sure if he is on the BioSQL or
> Open-Bio lists yet) has started work on parsing UniProt XML
> files for Biopython. Here the DE comment lines are already
> provided broken up with XML markup. Hopefully their nested
> structure matches what BioPerl was doing with the SwissProt
> DE lines.
>
> Regards,
>
> Peter
>