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Error with latest Reactome and Netpath biopax files
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Ruth  
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 More options Jul 3, 3:10 pm
From: Ruth <ruth.isser...@utoronto.ca>
Date: Fri, 3 Jul 2009 12:10:55 -0700 (PDT)
Local: Fri, Jul 3 2009 3:10 pm
Subject: Error with latest Reactome and Netpath biopax files
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Hi,
I have been re-building my instance of cpath and the reactome and
Netpath biopax files keep coming up with the following error:

Reading in file:  Mus musculus.owl
XML Type:  BIO_PAX
Reading in meta-data from:  db.info
Data source is:  Reactome
Reading in file content...
Processing file...
Validating BioPAX File with Paxtools...
rethrew: org.xml.sax.SAXParseException: Invalid byte 2 of 3-byte UTF-8
sequence.

Is there any way of fixing the files?

It works fine for Cell map, Biocarta and NCI biopax files.

Thanks,
Ruth


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Gary Bader  
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 More options Jul 3, 3:19 pm
From: Gary Bader <ba...@cbio.mskcc.org>
Date: Fri, 03 Jul 2009 15:19:54 -0400
Local: Fri, Jul 3 2009 3:19 pm
Subject: Re: Error with latest Reactome and Netpath biopax files
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Hi Ruth - what do the top of the files look like in a text editor?  Is
there an issue with them?

Gary

--
http://baderlab.org
Terrence Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

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Ruth Isserlin  
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 More options Jul 3, 3:31 pm
From: "Ruth Isserlin" <ruth.isser...@utoronto.ca>
Date: Fri, 3 Jul 2009 15:31:08 -0400
Local: Fri, Jul 3 2009 3:31 pm
Subject: RE: Error with latest Reactome and Netpath biopax files
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Hi Gary,

The tops of the files don't look different to me.  Reactome has a few more
things defined, not sure if that breaks them.

For Cellmap which works it looks like -
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bp="http:
//www.biopax.org/release/biopax-level2.owl#"
xmlns:owl="http://www.w3.org/2002/0
7/owl#" xmlns="http://cbio.mskcc.org/cpath#"
xml:base="http://cbio.mskcc.org/cpa
th">
  <owl:Ontology rdf:about="">
    <owl:imports
rdf:resource="http://www.biopax.org/release/biopax-level2.owl"/>
  </owl:Ontology>

And for Reactome it looks like -
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bp="http:
//www.biopax.org/release/biopax-level2.owl#"
xmlns:rdfs="http://www.w3.org/2000/
01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:xsd="http://www
.w3.org/2001/XMLSchema#" xmlns="http://www.reactome.org/biopax#"
xml:base="http:
//www.reactome.org/biopax">
  <owl:Ontology rdf:about="">
    <owl:imports
rdf:resource="http://www.biopax.org/release/biopax-level2.owl"/>
  </owl:Ontology>

Thanks,
Ruth


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Gary Bader  
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 More options Jul 3, 3:46 pm
From: Gary Bader <ba...@cbio.mskcc.org>
Date: Fri, 03 Jul 2009 15:46:05 -0400
Local: Fri, Jul 3 2009 3:46 pm
Subject: Re: Error with latest Reactome and Netpath biopax files
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I think you have to use a hex editor to see the if the actual bytes are
different.

Gary

--
http://baderlab.org
Terrence Donnelly Centre for Cellular and Biomolecular Research
University of Toronto

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Ethan Cerami  
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 More options Jul 3, 3:49 pm
From: Ethan Cerami <cer...@cbio.mskcc.org>
Date: Fri, 03 Jul 2009 15:49:07 -0400
Local: Fri, Jul 3 2009 3:49 pm
Subject: Re: Error with latest Reactome and Netpath biopax files
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I think that Ben uses a character conversion utility to fix this issue,
but he is on holiday today (it's the fourth of july vacation here today).


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rex.dw...@syngenta.com  
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 More options Jul 8, 2:32 pm
From: <rex.dw...@syngenta.com>
Date: Wed, 8 Jul 2009 14:32:25 -0400
Local: Wed, Jul 8 2009 2:32 pm
Subject: RE: Error with latest Reactome and Netpath biopax files
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I am having similar problems trying to read reactome files in BP level 3 programmatically with paxtools.
I don't understand - is this a bug in paxtools, or do the files need to be rebuilt with the right character set or something?
Does anyone know of level 3 files in the correct format?
Rex

From: cpath-dev@googlegroups.com [mailto:cpath-dev@googlegroups.com] On Behalf Of Ethan Cerami
Sent: Friday, July 03, 2009 3:49 PM
To: cpath-dev@googlegroups.com
Cc: gro...@cbio.mskcc.org
Subject: Re: Error with latest Reactome and Netpath biopax files

I think that Ben uses a character conversion utility to fix this issue, but he is on holiday today (it's the fourth of july vacation here today).

Gary Bader wrote:

I think you have to use a hex editor to see the if the actual bytes are

different.

Gary

Ruth Isserlin wrote:

Hi Gary,

The tops of the files don't look different to me.  Reactome has a few more

things defined, not sure if that breaks them.

For Cellmap which works it looks like -

<?xml version="1.0" encoding="UTF-8"?>

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<http://www.w3.org/1999/02/22-rdf-syntax-ns>

xmlns:bp="http:<http://www.biopax.org/release/biopax-level2.owl>

//www.biopax.org/release/biopax-level2.owl#"<http://www.biopax.org/release/biopax-level2.owl>

xmlns:owl="http://www.w3.org/2002/0<http://www.w3.org/2002/07/owl>

7/owl#"<http://www.w3.org/2002/07/owl> xmlns="http://cbio.mskcc.org/cpath#"<http://cbio.mskcc.org/cpath>

xml:base="http://cbio.mskcc.org/cpa<http://cbio.mskcc.org/cpath>

th"<http://cbio.mskcc.org/cpath>>

  <owl:Ontology rdf:about="">

    <owl:imports

rdf:resource="http://www.biopax.org/release/biopax-level2.owl"<http://www.biopax.org/release/biopax-level2.owl>

/>

  </owl:Ontology>

And for Reactome it looks like -

<?xml version="1.0" encoding="UTF-8"?>

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"<http://www.w3.org/1999/02/22-rdf-syntax-ns>

xmlns:bp="http:<http://www.biopax.org/release/biopax-level2.owl>

//www.biopax.org/release/biopax-level2.owl#"<http://www.biopax.org/release/biopax-level2.owl>

xmlns:rdfs="http://www.w3.org/2000/<http://www.w3.org/2000/01/rdf-schema>

01/rdf-schema#"<http://www.w3.org/2000/01/rdf-schema> xmlns:owl="http://www.w3.org/2002/07/owl#"<http://www.w3.org/2002/07/owl>

xmlns:xsd="http://www<http://www.w3.org/2001/XMLSchema>

.w3.org/2001/XMLSchema#"<http://www.w3.org/2001/XMLSchema> xmlns="http://www.reactome.org/biopax#"<http://www.reactome.org/biopax>

xml:base="http:<http://www.reactome.org/biopax>

//www.reactome.org/biopax"<http://www.reactome.org/biopax>>

  <owl:Ontology rdf:about="">

    <owl:imports

rdf:resource="http://www.biopax.org/release/biopax-level2.owl"<http://www.biopax.org/release/biopax-level2.owl>

/>

  </owl:Ontology>

Thanks,

Ruth


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