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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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> 
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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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