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

Rachel Drysdale rdrysdale at plos.org
Wed Mar 11 09:41:33 PDT 2015


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

[cid:image001.jpg at 01D05C1A.39199F70]

Any ideas?
Rachel

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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:



[cid:image003.png at 01D05C19.D747A940]



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

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



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

before you submit it.



Ray


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