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[bioontology-support] API Example Code in R

Jennifer Leigh Vendetti vendetti at
Fri Mar 10 12:29:22 PST 2017

Hello Scott,

On Mar 10, 2017, at 10:39 AM, Scott Keating <sjk3001 at<mailto:sjk3001 at>> wrote:

I am trying to get the annotator to work using the R programming system. The API Documentation found here<> states that sample code can be found in other languages. Do you happen to have example code written in R that I might be able to use as a reference?

This is our GitHub repository that contains sample code in various languages:

We didn’t provide anything in R (I don’t know of anyone on our current development team that knows R).  There is however, a link in the file that points to an R project authored by Cristian R. Munteanu:

It looks like he’s interacting with the Recommender instead of the Annotator, but I imagine the code may be of use to you.  There is also an old page on our wiki with some example Annotator code written in R:

The caveat here being that the page is roughly 4 years old, and I can see that it’s using an older version of our REST API.  So, this one may not turn out to be that useful.

I am attempting to annotate patient electronic health record data for symptoms of adverse drug events using the diabetes ontology. When I run my code it states “Error: Bad Request”, which I assume has something to do with my API key, which I have verified as correct and properly linked to my account. Any pointers?

You mentioned that you think there’s a problem with your API key.  Just curious - did you try to execute a simple curl request outside of your program to verify that your API key is working, e.g.:


Kind regards,

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