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[bioontology-support] [BioPortal] Feedback from KReinold

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Sep 17 15:31:57 PDT 2021


Hi Kathy,

Thanks for the clarification. I opened your TerraDCAT-AP.ttl ontology source file in Protege. I’m attaching a screenshot of the class trees in BioPortal and Protege side-by-side. Protege is also displaying these Error1, Error2, etc. classes.

Both Protege and BioPortal use the OWL API (https://github.com/owlcs/owlapi#readme) for loading ontologies. According to documentation on the Protege wiki, these Error classes are created by the OWL API when it encounters ontology documents that are valid RDF, but not valid OWL (https://protegewiki.stanford.edu/wiki/Protege4ErrorClasses). I would need to consult with one of our ontology development experts internally to get some assistance with what about your ontology isn’t valid OWL.

I understand from my colleague Marcos that you uploaded your ontology to BioPortal in order to access the terms in CEDAR. The handful of Error classes displayed in BioPortal don’t prevent the rest of your classes from being served by the application. You should be able to see all the other classes that don’t have an Error designation in CEDAR.

Kind regards,
Jennifer



[cid:994B683A-2AE8-4F99-B236-57FED2E8CE99 at lan]



On Sep 17, 2021, at 2:37 PM, Kathy Reinold <kreinold at broadinstitute.org<mailto:kreinold at broadinstitute.org>> wrote:

Ok, managed to update the submission and you can see the errors in the Classes page now.  For example, errors 10 and 11 should show that they are inheriting from DCAT entities.  See below.  This screen snapshot is from TopBraid Composer but Protege processes it correctly as well.


<Screen Shot 2021-09-17 at 5.37.04 PM.png>


Kathy Reinold
Lead, Data Modeling, Data Sciences Platform
The Broad Institute of MIT and Harvard
105 Broadway - 359M
Cambridge, MA 02142
(she/they)


On Fri, Sep 17, 2021 at 5:18 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Kathy,


On Sep 17, 2021, at 2:04 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Hello,
I tried submitting an ontology in OWL that imports two other vocabularies.
# imports: http://www.w3.org/ns/dcat
# imports: https://raw.githubusercontent.com/EBISPOT/DUO/master/duo-basic.owl
This produced errors.

Two questions:
1. Is there more information about the submission process available?

The only documentation we have is on our wiki here:

https://www.bioontology.org/wiki/BioPortal_Help#Submitting_an_ontology


2. I just realized dcat (which uses content negotiation for that link) is only capable of returning ttl, rdf and not native owl. Could that be the problem? If so, do you have any suggestions for addressing this?

I assume you’re referring to the ontology entry created under the acronym “TERRADCAT_AP” at this page:

https://bioportal.bioontology.org/ontologies/TERRADCAT_AP

Can you give any more detail about the error you encountered?

I’m looking at your ontology now and it looks like the submission was created as a "metadata only" submission, meaning that the classes and properties in your ontology wouldn’t be available for browsing via BioPortal. Is this what you intended?

Kind regards,
Jennifer



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