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[bioontology-support] [BioPortal] Feedback from fathalla

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Sep 30 16:30:40 PDT 2019


Hello,

I’ve been attempting to load / examine your ontology outside of the BioPortal system. I used a programmatic approach with the OWL API [1], and also tried manually opening the ontology file in the Protege ontology editing application [2]. In both cases, there are a number of errors. If you happen to use Protege, you can see them via Window | Show log… menu:


[cid:A1E90BDA-21B5-4F1C-8AED-BD3BF89522EB at stanford.edu]
Here is the complete text of one of the errors:

ERROR  16:16:32  Attempt to transform an axiom to correct misuse of properties failed. Property replacement: {<http://xmlns.com/foaf/0.1/name>=<http://xmlns.com/foaf/0.1/name>, <http://www.w3.org/2008/05/skos#prefLabel>=<http://www.w3.org/2008/05/skos#prefLabel>, <http://www.w3.org/2008/05/skos#hiddenLabel>=<http://www.w3.org/2008/05/skos#hiddenLabel>, <http://www.w3.org/2008/05/skos#definition>=<http://www.w3.org/2008/05/skos#definition>, <http://www.w3.org/2008/05/skos#altLabel>=<http://www.w3.org/2008/05/skos#altLabel>}, axiom: AnnotationAssertion(<http://www.w3.org/2008/05/skos#definition> <http://www.w3.org/2008/05/skos#hasTopConcept> "A top level concept in the concept scheme."@en), error: uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplPlain cannot be cast to org.semanticweb.owlapi.model.IRI

We can more readily help with getting an ontology uploaded / displaying properly in BioPortal when parsing errors like this aren’t present.

Kind regards,
Jennifer

[1] http://owlcs.github.io/owlapi/
[2] https://protege.stanford.edu/




On Sep 30, 2019, at 5:50 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: fathalla

Email: sm_fathalla at yahoo.com<mailto:sm_fathalla at yahoo.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fontologies%2FMODSCI%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fwww.w3.org<http://252Fwww.w3.org>%252F2003%252F01%252Fgeo%252Fwgs84_pos%2523SpatialThing

Feedback:

class names for my ontology do not appear well : http://bioportal.bioontology.org/ontologies/MODSCI/

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