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

John Graybeal jgraybeal at
Wed Jul 25 17:52:14 PDT 2018

George, all,

Following up with a bit more detail.

Please note you can find a few more recent articles about the annotator, or mentioning updates to the annotator, by searching for 'ncbo annotator'.

The support archives are on Nabble at

1) There have been a large number of changes in the Annotator since 2009, by a significant number of people. For example see the Contributors in GitHub at and the history tab at I think it would be difficult to summarize the changes, especially in this moment, since the principles are mostly in other positions or on vacation. But the Release Notes (and pointers to earlier release notes) are at, and you can search in your browser for 'annotat' to find many of the major changes summarized there. If you have more advanced questions after reviewing that material, contact us and we can try to put you in touch with the right people.

2) There are instructions for getting an API key on the BioPortal wiki:

3) The API documentation is indeed at Note the first section entries apply to many other sections.


On Jul 20, 2018, at 10:03 PM, John Graybeal <jgraybeal at<mailto:jgraybeal at>> wrote:

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<mailto:bioontology-support-bounces at>> on behalf of George Shannon <gjscnc at<mailto:gjscnc at>>
Sent: Friday, July 20, 2018 7:20:03 PM
To: support at<mailto: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>
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

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