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[bioontology-support] NCBO Annotator

John Graybeal jgraybeal at stanford.edu
Fri Nov 20 21:03:24 PST 2020


Hello,

No, with apologies there is no option in the UI like this. In the API you could choose to only 'look at' the first annotation for each term or phrase, and I believe choosing 'match longest' will eliminate matches of terms within other terms. But it the UI all annotations are returned.

I created ticket https://github.com/ncbo/bioportal-project/issues/192 to capture this issue. Thank you for your request!

John

On Nov 19, 2020, at 2:37 PM, Pranhav Sundararajan <pranhav16 at gmail.com<mailto:pranhav16 at gmail.com>> wrote:

Hello,

The NCBO annotator sometimes annotates the same word multiple times, and I was wondering if there would be any setting to have every word only be annotated once?

Thank you

On Tue, Nov 17, 2020 at 6:14 PM Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Pranhav,

Thank you for contacting us. Please check out or REST sample code repository here:

https://github.com/ncbo/ncbo_rest_sample_code

The Annotator java example can be referenced from here:

https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/AnnotateText.java

Doing a quick Github search for “ncbo annotator” also yields a number of code sources that reference our Annotator REST API that you could adopt in your application:

https://github.com/search?q=ncbo+annotator

Hope this helps and you find the code you are looking for!

Michael


On Nov 17, 2020, at 9:25 AM, Pranhav Sundararajan <pranhav16 at gmail.com<mailto:pranhav16 at gmail.com>> wrote:

Hello,

I'm trying to use the NCBO Annotator in a program that will allow for multiple datasets and files to be annotated. Where can I find the code that will allow me to use the Annotator programmatically?

Thank you
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========================
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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