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[bioontology-support] Help with bioontology virtual machine

Jennifer Leigh Vendetti vendetti at stanford.edu
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,
Jennifer


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

Hi,
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 http://data.bioontology.org/annotator, I get the output I care about with all the annotations, but if I query my local instance like so http://192.168.1.132/annotator
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.

Thanks

Chaitanya


[https://lh5.googleusercontent.com/iYAOors3sipDiaMVVlLOYryK-aMZXrJJlQ3adHayqmU0RPdOKD9MheNofOXdpiVpvCF2j2iEYXjgU7UrTuuKDW6yuU-_KCnECSksLBGM-3v1ulPSPI-Gju23TB102leR3bqI1Cfc]

Dr. Chaitanya Churi
Senior Data Scientist
chaitanya at lumiata.com<mailto:chaitanya at lumiata.com>
www.lumiata.com<http://www.lumiata.com/>

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