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[bioontology-support] Request for information - API key for bio-ontology annotator and technical information

John Graybeal jgraybeal at
Fri Jul 20 22:03:01 PDT 2018

A few quick thoughts before disappearing for the weekend:
1) yes, though there might have been an improvement or two since then.
2) when you register for BioPortal you get an API key that works for all tools (on your profile page).
3) yes. If you search for ‘BioPortal api’ I think the first hit is the API documentation.

You might want to review the support archives on nabble (search google again) for related topics, and the BioPortal release notes (google…) re annotator upgrades.

Sorry, can’t provide examples, pilot says I must go now!


From: bioontology-support <bioontology-support-bounces at> on behalf of George Shannon <gjscnc at>
Sent: Friday, July 20, 2018 7:20:03 PM
To: support at
Cc: Corns, Steven; Donald C. Wunsch
Subject: [bioontology-support] Request for information - API key for bio-ontology annotator and technical information

I am a volunteer research member of the Systems Engineering Dept. and the Applied Computational Intelligence Lab at the Missouri University of Science and Technology (MST).

I am investigating entity recognition methods, and wish to perform comparisons of existing methods against an innovative approach we have developed biomedical text. We use an ontology-based approach, principally SNOMED-CT.

I'm contacting you for technical information regarding use of the annotator REST-full service.

As I understand it, this service is the Open Biomedical Annotator as described in Jonquet C, Shah NH, Musen MA. The Open Biomedical Annotator. Summit on Translational Bioinformatics. 2009;2009:56-60.  This papers notes use of the MGrep method for identifying medical entities in text.

Would you mind helping me in three area: 1) confirm use of the MGrep entity recognizer, 2) can I obtain an API key for use of the annotator via the REST interface, and 3) does a parameter exist in the API for limiting results to a particular ontology?

I would greatly appreciate your help.

Best Regards,


George J. Shannon, PhD SE
Missouri University of Science and Technology
(314) 550-5589 (cell)
gjscnc at
<mailto:gjscnc at>
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