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

Ray Fergerson ray.fergerson at stanford.edu
Wed Mar 11 14:07:46 PDT 2015


I would suggest OWL2. The extension for such a file (OWL/RDF) should be
“.owl” though and not “.txt”. I am not familiar with this dialog box. From
what application is it? It doesn’t look like Protégé to me. If your native
format is “.obo” then we can read that directly.



Ray



From: bioontology-support
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Rachel Drysdale
Sent: Wednesday, March 11, 2015 8:02 AM
To: Ray Fergerson; support at bioontology.org
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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