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[bioontology-support] NCBO Annotator Excel plug-in

Clement Jonquet jonquet at
Fri Oct 30 09:52:12 PDT 2015

Hi all, 


I am re-opening that thread question Eamonn about the possibility to use OntoMaton with another BioPortal appliance.


We are working on a agronomic/plant specific version of BioPortal, called AgroPortal and some of our users at INRA will love to see the Plugin being able to talk to our /search and /annotator services.


We have made some improvement to the Annotator (e.g., scoring) but we are completely backward compatible with NCBO. So I guess this would be just a small change in the code to hit another web service endpoint.


Eamonn, does it sound reasonable to you ? 

Can you point us to the exact spot in the GitHub OntoMaton repo here to change?





De : Eamonn Maguire [mailto:eamonn.maguire at] 
Envoyé : mercredi 5 mars 2014 02:40
À : Ray Fergerson <ray.fergerson at>; Clement Jonquet <jonquet at>
Cc : support at; ISA Team <isatools at>
Objet : RE: [bioontology-support] NCBO Annotator Excel plug-in


Thanks Ray,

This is great! :)

Best wishes,


Sent from my Windows Phone


From: Ray Fergerson <mailto:ray.fergerson at> 
Sent: ‎04/‎03/‎2014 23:24
To: Eamonn Maguire <mailto:eamonn.maguire at> ; Clement Jonquet <mailto:jonquet at> 
Cc: support at <mailto:support at> ; ISA Team <mailto:isatools at> 
Subject: RE: [bioontology-support] NCBO Annotator Excel plug-in

The release today allows you to specify that you want the preferred name for every annotated class. Try this tomorrow.




From: bioontology-support-bounces at <mailto:bioontology-support-bounces at>  [mailto:bioontology-support-bounces at] On Behalf Of Eamonn Maguire
Sent: Tuesday, March 4, 2014 3:19 AM
To: Clement Jonquet
Cc: support at <mailto:support at> ; ISA Team
Subject: Re: [bioontology-support] NCBO Annotator Excel plug-in


This email skipped under my radar, apologies.


The current version still uses the old version of the annotator. As it stands, without the update to the annotator to include the term name in the response, it’s currently not usable (too slow to then search for each term, it’s preferred name). e.g. <>  - from the results here, there is no way of knowing what the actual term is - we have to do an additional query per term to figure that out - that’s way too many queries to have to do and would make the service unusable.


Is there any chance this can be updated ASAP? We’re in the process of  releasing OntoMaton 2, which uses the new bioportal services, but we haven’t updated the annotator service as of yet, until this fix is made.


Best wishes,




On 13 Feb 2014, at 08:54, Clement Jonquet <jonquet at <mailto:jonquet at> > wrote:


Thanks Trish for this response.


Hi Eamonn,

Do you confirm the Ontomaton tool is still available and use the new NCBO Annotator API (i.e., the one in BP 4.0) described at:






De : Trish Whetzel [ <mailto:plwhetzel at> mailto:plwhetzel at] 
Envoyé : jeudi 6 février 2014 17:21
À : Clement Jonquet
Cc :  <mailto:support at> support at
Objet : Re: [bioontology-support] NCBO Annotator Excel plug-in


Hi Clement,

As I recall, the Excel plugin for the Annotator was no longer being maintained. However, you might be interested to check-out OntoMaton [1], which is an Excel GoogleDoc script that incorporates the BioPortal Search and Annotator services.


[1]  <>


On Thu, Feb 6, 2014 at 12:23 AM, Clement Jonquet < <mailto:jonquet at> jonquet at> wrote:

Hi all,


We used to have an Excel plugin for the Annotator.

Does anyone have updates on this ?


Is it still available ?

Is it compatible with Annotator 2 ?






Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor

PI of the  <> SIFR project: Semantic Indexing of French Biomedical Data Resources (ANR, UM2, CNRS, IBC)

Organizer of  <> Web Science Montpellier Meetup


 <mailto:jonquet at> jonquet at



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