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[bioontology-support] NCBO Virtual Appliance configuration with RadLex

Kulkarni, Rushikesh RushikeshKulkarni at mednet.ucla.edu
Wed Sep 30 15:07:43 PDT 2020


Hi Michael,

Thank you for your prompt reply! I followed your steps and able to set RadLex’s preferred name and other properties.

I am fairly new to NCBO virtual appliance and have some questions regarding appliance ID and its registration. Would you be able to answer it?
Here are my questions,

1.       How do I get the appliance ID required to register appliance? I tried http://{my-appliance-hostname}/admin#licensing but, it took me to login page.

2.       Is there any default admin credential which gets created during virtual appliance setup? Or How do I create admin account?

Once again, Thank you for all you help.

Regards,
Rushi

From: Michael Dorf <mdorf at stanford.edu>
Sent: Wednesday, September 30, 2020 1:29 PM
To: John Graybeal <jgraybeal at stanford.edu>
Cc: Kulkarni, Rushikesh <RushikeshKulkarni at mednet.ucla.edu>; support at bioontology.org
Subject: Re: [bioontology-support] NCBO Virtual Appliance configuration with RadLex


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Hi Rushi,

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

[cid:image002.png at 01D6972F.B7409B50]

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,

Michael



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

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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