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[bioontology-support] R script for term mapping using NCBO Recommender
Paul R Alexander
palexander at stanford.edu
Mon Jul 14 11:19:14 PDT 2014
Thanks Cristian. I’ve added a link to your project from our Code Sample repository here:
https://github.com/ncbo/ncbo_rest_sample_code
This is especially useful because we don’t currently have any R programmers on staff and so have no examples. Thanks again!
Paul
On Jul 13, 2014, at 4:04 PM, Munteanu Cristian <muntisa at gmail.com> wrote:
> 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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> Today's Topics:
>
> 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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