Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] [BioPortal] Feedback from fathalla

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


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]
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: {<>=<>, <>=<>, <>=<>, <>=<>, <>=<>}, axiom: AnnotationAssertion(<> <> "A top level concept in the concept scheme."@en), error: 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,


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

Name: fathalla

Email: sm_fathalla at<mailto:sm_fathalla at>



class names for my ontology do not appear well :

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot 2019-09-30 16.17.16.png
Type: image/png
Size: 319225 bytes
Desc: Screenshot 2019-09-30 16.17.16.png
URL: <>

More information about the bioontology-support mailing list