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[bioontology-support] R script for term mapping using NCBO Recommender

Munteanu Cristian muntisa at gmail.com
Sun Jul 13 16:04:32 PDT 2014


I programmed an R script that can map a list of terms into all ontologies
using NCBO Recommender (there is a score for each map). I hope somebody
will find it useful:

https://github.com/muntisa/RNCBO

Best regards,
Cristian R. Munteanu

Senior Postdoctoral Researcher
www.enanomapper.net
Department of Bioinformatics - BiGCaT
Faculty of Health, Life Sciences and Medicine
Maastricht University
www.bigcat.unimaas.nl
ORCID: 0000-0002-5628-2268


On Fri, Jul 11, 2014 at 9:03 PM, <
bioontology-support-request at lists.stanford.edu> wrote:

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>    1. Tools and scripts to generate mappings in a VA (Clement Jonquet)
>    2. [BioPortal] Feedback from HanfeiBao (support at bioontology.org)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 11 Jul 2014 18:47:53 +0200
> From: "Clement Jonquet" <jonquet at lirmm.fr>
> To: <support at bioontology.org>
> Subject: [bioontology-support] Tools and scripts to generate mappings
>         in a VA
> Message-ID: <07f101cf9d27$dbceeb10$936cc130$@lirmm.fr>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi all,
>
>
>
> I am wondering where are the scripts/tools you guys used to generate
> mappings btw ontologies.
>
> Are they somewhere on GitHub or in the VA ?
>
>
>
> For instances:
>
> - I am hosting several OBO ontologies in my local appliance and they
> contains "xref:" properties that represent mappings to other ontologies.
>
> - I am hosting several UMLS ontologies that offer cui property that that
> represent mappings to other ontologies.
>
>
>
> Are those scripts available ?
>
> Can some of them be automated when an ontology is parsed to be included in
> BioPortal ?
>
>
>
> Thank you
>
> Clement
>
>
>
>
>
>
> ----------------------------------------------------------------------------
> -----------------------------------------------
>
> Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
>
> PI of the  <http://www.lirmm.fr/sifr/> SIFR project: Semantic Indexing of
> French Biomedical Data Resources (ANR, UM2, CNRS, IBC)
>
> Organizer of  <http://www.meetup.com/webscience-montpellier/> Web Science
> Montpellier Meetup
>
>
>
>  <mailto:jonquet at lirmm.fr> jonquet at lirmm.fr
>
>  <http://www.lirmm.fr/~jonquet> 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:
> <http://twitter.com/jonquet_lirmm> @jonquet_lirmm
>
>                 France
> Google:                <mailto:jonquet.lirmm at gmail.com>
> jonquet.lirmm at gmail.com
>
>
> ----------------------------------------------------------------------------
> ------------------------------------------
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> ------------------------------
>
> Message: 2
> Date: Fri, 11 Jul 2014 09:50:54 -0700
> From: support at bioontology.org
> To: support at bioontology.org,     hanfeib at gmail.com
> Subject: [bioontology-support] [BioPortal] Feedback from HanfeiBao
> Message-ID:
>
> <53c015ee56189_76083fb10ba4fd4816f at ncbo-prd-app-18.stanford.edu.tmail>
> Content-Type: text/plain; charset=utf-8
>
>
> Name: HanfeiBao
>
> Email: hanfeib at gmail.com
>
> Location: http://bioportal.bioontology.org/ontologies/HIVO004
>
> Comment:
> Hi, I have made 3 uploads today, but the first 2 uploads are mistakes
> (only the last one is correct). Please help me to delete the mistake
> uploads.
>
> Thank you.
>
> Hanfei bao
> (mail:hanfeib at gmail.com )
>
>
>
> ------------------------------
>
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