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[bioontology-support] Help with bioontology virtual machine

Jennifer Leigh Vendetti vendetti at
Thu Nov 9 11:35:47 PST 2017

Hello Dr. Churi,

I’m wondering if you could provide us with more information.

- What ontologies have you loaded into the Virtual Appliance? If you’ve loaded any, they would be listed on the ontology browse page (Tools -> Ontology Browser).

- Are you able to see any results from the Annotator in the user interface of your appliance?

We spun up a test instance of the appliance here, loaded 4 ontologies (NCIT, RADLEX, GO, and STY), and tried reproducing this problem. The annotator service worked as expected.

Kind regards,

On Nov 7, 2017, at 12:00 PM, Chaitanya Churi <chaitanya at<mailto:chaitanya at>> wrote:

I’m working with the virtual machine installation of the bioontology portal (specifically the third Release Candidate (Version 2.5 Release Candidate 3)).

I’m querying the annotator endpoint and I’m having trouble with the output.

If I query the regular bioportal api at, I get the output I care about with all the annotations, but if I query my local instance like so
with the same exact API call, I get back only a list of semantic types and no annotations. Is the output format for this version different? Is there updated documentation for this?

Appreciate your help.




Dr. Chaitanya Churi
Senior Data Scientist
chaitanya at<mailto:chaitanya at><>

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