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

[Allen Day]

what release are you referring to, with URL please?  i am looking here, 
and it is the same old iprscan with the bugs:

ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/RELEASE/3.3/

-allen


On Tue, 7 Dec 2004, Heikki Lehvaslaiho wrote:

> 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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> 
>