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[bioontology-support] NCBO Annotator Excel plug-in

Ray Fergerson ray.fergerson at stanford.edu
Tue Mar 4 15:24:17 PST 2014


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



Ray



From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Eamonn Maguire
Sent: Tuesday, March 4, 2014 3:19 AM
To: Clement Jonquet
Cc: support at bioontology.org; 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.
http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+o
f+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+
and+the+eye.
<http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+
of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel
+and+the+eye>  - 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,



Eamonn



On 13 Feb 2014, at 08:54, Clement Jonquet <jonquet at lirmm.fr> 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:

 <http://data.bioontology.org/documentation#nav_annotator>
http://data.bioontology.org/documentation#nav_annotator



Regards

CJ



De : Trish Whetzel [ <mailto:plwhetzel at gmail.com>
mailto:plwhetzel at gmail.com]
Envoyé : jeudi 6 février 2014 17:21
À : Clement Jonquet
Cc :  <mailto:support at bioontology.org> support at bioontology.org
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.

Cheers,

Trish
[1]
<http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-s
earch-tagging-for-google-spreadsheets/>
http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-se
arch-tagging-for-google-spreadsheets/



On Thu, Feb 6, 2014 at 12:23 AM, Clement Jonquet <
<mailto:jonquet at lirmm.fr> jonquet at lirmm.fr> 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 ?



Clement





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