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[bioontology-support] [BioPortal] Feedback from Rachel.Drysdale

Ray Fergerson ray.fergerson at stanford.edu
Wed Mar 11 14:11:12 PDT 2015


This is the same error (see RDF/XML below). The way the validator works is
that it first tries to identify the file format from the extension. If
this fails then it runs all possible parsers over the input. That is why
you see the results from multiple parsers.

 

The best way forward if the native format is OBO is just to submit the OBO
file (with extension .obo). If the native format is something else then
export as OWL 2, ensure that the extension is ".owl" and then validate
this file.

 

Ray

 

From: Rachel Drysdale [mailto:rdrysdale at plos.org] 
Sent: Wednesday, March 11, 2015 9:42 AM
To: Ray Fergerson; support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale

 

PS I tried the OWL 2 export (came out as a .txt file) and uploaded that
but still get "Error Rdf" statement and here is what validate_ontology
produced

 



 

Any ideas?

Rachel

 

PLOS I OPEN FOR DISCOVERY

Rachel Drysdale Ph.D. I Taxonomy Manager

ORCID:  <http://orcid.org/0000-0003-3037-0216> 0000-0003-3037-0216

Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom

 <mailto:rdrysdale at plos.org> rdrysdale at plos.org I Main +44 (0) 1223-442810

 <http://www.plos.org/> plos.org I  <http://www.facebook.com/PLoS.org>
Facebook I  <http://twitter.com/PLOS> Twitter I  <http://blogs.plos.org/>
Blog

 

 

 

From: Rachel Drysdale 
Sent: 11 March 2015 15:02
To: Ray Fergerson; support at bioontology.org
Cc: Rachel Drysdale
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale

 

Hi Ray,

 

>Essentially you have created a URL that contains 2 "#" characters. I
don't think that this is allowed.

 

This appears to be a feature of all 'Related Term' fields in the OWL
export of our thesaurus.

So there are 1142 such cases.

 

So I could go to our vendor to query this feature of the OWL export
option, or (possibly most expedient way out) I could ask you if any of the
other export formats on offer would do instead.  Here is the full range:

 



 

What do you think?

 

Thanks for further help

Rachel

 

PLOS I OPEN FOR DISCOVERY

Rachel Drysdale Ph.D. I Taxonomy Manager

ORCID: 0000-0003-3037-0216

Carlyle House, Carlyle Road, Cambridge CB4 3DN | United Kingdom

rdrysdale at plos.org I Main +44 (0) 1223-442810

plos.org I Facebook I Twitter I Blog

 

 

 

-----Original Message-----
From: Ray Fergerson [mailto:ray.fergerson at stanford.edu] 
Sent: 10 March 2015 21:43
To: Rachel Drysdale; support at bioontology.org
Subject: RE: [bioontology-support] [BioPortal] Feedback from
Rachel.Drysdale

 

Sorry for the long delay. We finally have this figured out.

 

The error in the file, that prevents parsing is:

 

----------

org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException:

[line=121:column=41] IRI '#T#T8798' cannot be resolved against current

base IRI  <http://localhost/owlfiles/plosthes.2014-5/>
http://localhost/owlfiles/plosthes.2014-5/ reason is: Illegal

character in fragment at index 2: #T#T8798

Validator has been updated to pick this up now. Passing to Ray Fergerson

for user contact.

----------------

 

Essentially you have created a URL that contains 2 "#" characters. I don't

think that this is allowed.

 

We have also fixed the problem with our validator. It is accessible at:

 

 <http://bioportal.bioontology.org/validate_ontology_file>
http://bioportal.bioontology.org/validate_ontology_file

 

This device should allow you to detect other errors in your ontology

before you submit it.

 

Ray

 

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