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[bioontology-support] NCBO Virtual Appliance configuration with RadLex

John Graybeal jgraybeal at stanford.edu
Wed Sep 30 13:18:22 PDT 2020


Rushi,

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

John

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

Hello,

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.

Regards,
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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