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[bioontology-support] NCBO Virtual Appliance configuration with RadLex

Michael Dorf mdorf at
Wed Sep 30 13:29:24 PDT 2020

Hi Rushi,

Try setting the Preferred Name, Synonym, and Definition properties under “advanced OWL options” via the “Edit Submission Information” page to these:


Once you hit “Save Submission”, your ontology should re-process automatically within 15 minutes or so and your tree should appear correctly. If it still doesn’t try re-processing the ontology manually after you’ve set the advanced OWL options.

Let me know if this helps.

Thank you,


On Sep 30, 2020, at 1:18 PM, John Graybeal <jgraybeal at<mailto:jgraybeal at>> wrote:


Thanks for the great problem report, I'm sorry for your trouble. We'll look into this right away.


On Sep 30, 2020, at 10:32 AM, Kulkarni, Rushikesh <RushikeshKulkarni at<mailto:RushikeshKulkarni at>> wrote:


I am trying to integrate Radiology Lexicon ontology with locally running NCBO Virtual appliance. I was able to import RadLax 4.0 OWL using 'Submit Ontology' functionality from Ontoportal UI.
But, somehow class names are not configured correctly. RID0, RID1, RID3 .. etc. are showing up under preferred name and as well as under class tree structure. (attached screenshot for reference)
For example, RID3 is showing under class structure and for Preferred Name field, instead of 'anatomical entity'.
Can you please help me with this issue?

I tried following things to debug the issue,

  1.  Tried to integrate RadLex using Ontoportal UI as well as with bioportal_ontologies_import.rb script.
  2.  Checked parsed ontology status using Rest service and it has following status "submissionStatus": ["RDF","OBSOLETE","INDEXED_PROPERTIES","METRICS","RDF_LABELS","UPLOADED","ANNOTATOR","INDEXED"]
  3.  Imported another ontology (Cell Ontology CL) and it has been set up correctly with no issue. This is just to test my local virtual machine.

Thanks in advance.

Rushi Kulkarni
UCLA Health


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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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