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[bioontology-support] recommendations for using the NCBO Annotator

John Graybeal jgraybeal at
Tue Feb 7 20:28:16 PST 2017

From: Leyla Jael García Castro <leylajael at<mailto:leylajael at>>

By the way, do you have a set of good practices to avoid service denial? We plan to annotate a large number of texts so just trying to figure it out how to get the best of the service without stressing it.

Hi Leyla,

I have created a document with recommendations for setting up a system for sending large amounts of (arguably large) queries to the NCBO Annotator. It is at

It also includes recommendations for troubleshooting issues accessing the Annotator via the API.

I have written this document largely by analysis, and have not done the proper systematic experiments to confirm its recommendations. I welcome any measurements, comments, or other insight from you, or other users of the Annotator.

As this page also is relevant for other API resources, similar experiences with them are welcome as well.


John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
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