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[bioontology-support] NCBO Annotator Excel plug-in

Trish Whetzel plwhetzel at gmail.com
Fri Oct 30 16:22:56 PDT 2015


Hi Clement,

Eamonn is with a different group now. I added in Philippe, who I think is
still in the same group.

Cheers,
Trish


On Fri, Oct 30, 2015 at 9:52 AM, Clement Jonquet <jonquet at lirmm.fr> wrote:

> 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?
>
>
>
> By,
>
> Clement
>
>
>
> *De :* Eamonn Maguire [mailto:eamonn.maguire at st-annes.ox.ac.uk]
> *Envoyé :* mercredi 5 mars 2014 02:40
> *À :* Ray Fergerson <ray.fergerson at stanford.edu>; Clement Jonquet <
> jonquet at lirmm.fr>
> *Cc :* support at bioontology.org; ISA Team <isatools at googlegroups.com>
> *Objet :* RE: [bioontology-support] NCBO Annotator Excel plug-in
>
>
>
> Thanks Ray,
>
> This is great! :)
>
> Best wishes,
>
> Eamonn
>
> Sent from my Windows Phone
> ------------------------------
>
> *From: *Ray Fergerson <ray.fergerson at stanford.edu>
> *Sent: *‎04/‎03/‎2014 23:24
> *To: *Eamonn Maguire <eamonn.maguire at st-annes.ox.ac.uk>; Clement Jonquet
> <jonquet at lirmm.fr>
> *Cc: *support at bioontology.org; ISA Team <isatools at googlegroups.com>
> *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.
>
>
>
> Ray
>
>
>
> *From:* bioontology-support-bounces at lists.stanford.edu [
> mailto:bioontology-support-bounces at lists.stanford.edu
> <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+of+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
>
>
>
> Regards
>
> CJ
>
>
>
> *De :* Trish Whetzel [mailto:plwhetzel at gmail.com <plwhetzel at gmail.com>]
> *Envoyé :* jeudi 6 février 2014 17:21
> *À :* Clement Jonquet
> *Cc :* 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-search-tagging-for-google-spreadsheets/
>
>
>
> On Thu, Feb 6, 2014 at 12:23 AM, Clement Jonquet <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
>
>
>
>
>
>
> ---------------------------------------------------------------------------------------------------------------------------
>
> Dr. *Clement JONQUET*  -  *PhD in Informatics  -  Assistant Professor*
>
> *PI of the SIFR project <http://www.lirmm.fr/sifr/>: Semantic Indexing of
> French Biomedical Data Resources (ANR, UM2, CNRS, IBC)*
>
> *Organizer of Web Science Montpellier
> <http://www.meetup.com/webscience-montpellier/> Meetup*
>
>
>
> jonquet at lirmm.fr
>
> http://www.lirmm.fr/~jonquet
>
>
>
>                 *University of Montpellier*                          Tel:
>                      +33/4 67 14 97 43
>
>
> LIRMM                                                            Fax:
>         +33/4 67  41 85 00
>
>                 161 rue Ada
>                                                   Skype:
>        clementpro
>                 34095 Montpellier Cdx
> 5                            Twitter:               @jonquet_lirmm
> <http://twitter.com/jonquet_lirmm>
>
>
> France                                                            Google:
>               jonquet.lirmm at gmail.com
>
>
> ----------------------------------------------------------------------------------------------------------------------
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