[Bioperl-l] Fw: bad entries in interpro again (fwd)

[Heikki Lehvaslaiho]

This came up last week and it turned out that the new release made available 
on Monday already had all double quotes escaped.

Download the new interpro.

	-Heikki


On Tuesday 07 December 2004 03:59, Jared Fox wrote:
> The problem with Interpro XML is that there are entries like:
>
>  <match id="SSF46785" name=""Winged helix" DNA-binding domain"
> dbname="SUPERFAMILY">
>
> or
>
> <match id="SSF55486" name="Metalloproteases ("zincins"), catalytic domain"
> dbname="SUPERFAMILY">
>
> The double quotes are supposed to mark the beginning and end of the name
> attribute, but the xml is not valid so it has double quotes inside the
> attribute itself. I believe this also happens with other illegal xml
> characters.
>
> If Interpro were to start producing valid XML, everything should work
> happily.
>
> > ---------- Forwarded message ----------
> > Date: Wed, 01 Dec 2004 16:16:46 +0000
> > From: Mikko Arvas <Mikko.Arvas at vtt.fi>
> > To: bioperl-l at portal.open-bio.org, Hilmar Lapp <hlapp at gmx.net>,
> >     Allen Day <allenday at ucla.edu>
> > Subject: bad entries in interpro again
> >
> > Hi,
> >
> > we've been discussing the problems of interpro parsing. I have a friend
> > who
> > is going to interpro consortium meeting next week and I could send some
> > regards through him. After reading your e-mails, I am (being quite a
> > newbie) a little bit confused of what kind of regards would you like to
> > send if any?
> >
> > Is the &apos the source of the problem? Is it really a problem in BioPerl
> > or in expat? Is somebody trying to solve the problem for Bioperl now
> > and is there any sensible thing that the interpro team could do to help?
> >
> > Cheers,
> > mikko
> >
> > Mikko Arvas
> > VTT Biotechnology
> >
> > e-mail:            mikko.arvas at vtt.fi
> > tel:                 +358-(0)9-456 5827
> > mobile:           +358-(0)44-381 0502
> > fax:                +358-(0)9-455 2103
> > mail:               Tietotie 2, Espoo
> >                       P.O. Box 1500
> >                       FIN-02044 VTT, Finland
>
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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