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[bioontology-support] NCBO Annotator VM Question

John Graybeal jgraybeal at
Fri Apr 3 11:31:36 PDT 2020


Offhand, I can't remember any significant code changes that would result in a change in annotation behavior since the 2.5 release. I looked at the release notes for BioPortal—nothing mentioned Annotator since 2.5 release of the Virtual Appliance—and tickets, which showed nothing in that time frame.

Things that can produce different content would include different versions of the ontologies, or possibly different indexing of the ontologies, which could be caused by an issue in the indexing processing. (We sometimes have intermittent indexing issues which disappear when we index the ontology again.)  It can also be the case that deprecated terms are not removed from our index until we re-index all the ontologies.

If you send us the example of your two responses, we can look closely at them and give you more specific feedback.


On Apr 2, 2020, at 12:31 PM, Megan R Barnes <mrbarnes at<mailto:mrbarnes at>> wrote:

Hello BioPortal Support,

I’m writing with a question about the VMWare Virtual Appliance.  We are running the v2.5 of the virtual appliance for the Annotator API, looking to reproduce results that we got from the BioPortal Annotator API.  I am aware that this is not the same version of the annotator that is running at , and have noticed that the shape of the API response is different between the two versions.  This is fine, but I have noticed that the content of the annotation responses is also different, even though I am using ontologies downloaded directly from<>.  Is there any obvious reason why the same ontologies would return different results in different versions of the annotator API?

Thanks for your help,

Megan Barnes
PhD Student in Computational Linguistics
University of Washington

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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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