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[bioontology-support] [BioPortal] Feedback from Karin Colsman

John Graybeal jgraybeal at
Thu Apr 29 13:26:22 PDT 2021


The issue we found seems to be with line 665, which declares that the IRI '' is an AnnotationProperty. I'm not sure why this is an error (likely because the IRI is also used as the object of all the importedFrom triples of dct:); but if we delete that line we find the ontology loads properly into BioPortal. (We have uploaded it as the latest version with this change.)  We checked the last version that loaded correctly, and it does not have this declaration.

663  ###
665  dct: rdf:type owl:AnnotationProperty .

We suggest that you might want to remove that line from future submissions in order that they parse in BioPortal.

We found the issue when running our OWL API wrapper code against this ontology. (That's just a command line wrapper for the OWL API library.)  I'm wondering if you might be running a different version of the OWL API library, to explain why you didn't see a parsing issue?  We are running 4.5.17.

Please let us know of concerns or questions.


On Apr 26, 2021, at 1:39 AM, Karin Colsman <karin.colsman.contractor at<mailto:karin.colsman.contractor at>> wrote:

Dear support team,

we are getting an RDF error while trying to upload a new version of the AFO ontology at

The ttl file can be opened both with the OWL API and the JENA API (Java versions) without any errors. Can you see from your server logs what the problem might be?

I am also attaching a screenshot of the support form which is unusable, because the site footer is overlapping the form fields. My screen resolution is 1920x1080. I have tried Firefox, Chrome and Internet Explorer and the problem is present on all of them.

Thank you very much for your time,

Karin Colsman

From: support at<mailto:support at> <support at<mailto:support at>>
Sent: Monday, 24 August, 2020 10:24
To: support at<mailto:support at>; Karin Colsman <karin.colsman.contractor at<mailto:karin.colsman.contractor at>>
Subject: [BioPortal] Feedback from Karin Colsman

Name: Karin Colsman

Email: karin.colsman.contractor at<mailto:karin.colsman.contractor at>


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John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360

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