W3C home > Mailing lists > Public > public-lod@w3.org > February 2012

Re: How do OBO ontologies work on the LOD?

From: Kerstin Forsberg <kerstin.l.forsberg@gmail.com>
Date: Wed, 22 Feb 2012 00:43:15 +0100
Message-Id: <FBA4A24C-DA33-4658-81A9-BE928C018CDF@gmail.com>
Cc: Juan Sequeda <juanfederico@gmail.com>, "public-lod@w3.org" <public-lod@w3.org>, Peter DeVries <pete.devries@gmail.com>
To: Alan Ruttenberg <alanruttenberg@gmail.com>, "mcourtot@gmail.com" <mcourtot@gmail.com>
Hi Alan and Melaine,
I think you could provide some clarity to the discussion below. 

I spontaneously think about MIREOT - Minimum information to reference an external ontology term
http://obi-ontology.org/page/MIREOT

And, I also wonder if Bernard Vatant's proposal for 5-stars of link vocabolaries is applicacable also for OBO foundry based ontolgies?
http://blog.hubjects.com/2012/02/is-your-linked-data-vocabulary-5-star_9588.html 

Kind regards
Kerstin Forsberg
@kerfors

21 feb 2012 kl. 21:51 skrev Peter DeVries <pete.devries@gmail.com>:

> Hi Juan,
> 
> Thanks for this. I read the paper. They have an "OWL" version of this OBO vocabulary but it seems to not be a fully mapped OWL version as described in your paper.
> 
> In this particular use case I was thinking of applying the terms and properties described by the ontology to my species concepts.
> 
> For instance:
> 
> species X has this metabolic pathway.  (which would be useful for finding species with potential drug interactions or other chemical reactions)
> 
> I don't think this use case requires the full OBO  relationships, just a mapping ontology that connects terms and characters to those in the OBO ontology.
> 
> Doing it this way you might get a species "tagged" with something that is not appropriate but that could be detected by some service that analyzes the statements made
> in the species concept markup.
> 
> My guess is that some of the OBO ontologies (if fully entailed) will not play well on the LOD cloud, but they would play a useful role when mapped as I described.
> 
> Does my interpretation seem appropriate to you or am I missing something?
> 
> Thanks,
> 
> - Pete
> 
> 
> 
> On Tue, Feb 21, 2012 at 9:39 AM, Juan Sequeda <juanfederico@gmail.com> wrote:
> Peter
> 
> You may want to take a look at this:
> http://www.ncbi.nlm.nih.gov/pubmed/21388572
> 
> The implementation of the OBO to OWL mapping work is part of official Gene Ontology project.
> 
> Juan Sequeda
> +1-575-SEQ-UEDA
> www.juansequeda.com
> 
> 
> 
> On Mon, Feb 20, 2012 at 7:46 PM, Peter DeVries <pete.devries@gmail.com> wrote:
> How do OBO type ontologies work in the Linked Open Data cloud.
> 
> One that I recently loaded has a large number of blank nodes.
> 
> It the idea that these will be mapped to LOD URI's?
> 
> Thanks,
> 
> - Pete
> 
> -- 
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries@wisc.edu
> TaxonConcept  &  GeoSpecies Knowledge Bases
> A Semantic Web, Linked Open Data  Project
> --------------------------------------------------------------------------------------
> 
> 
> 
> 
> -- 
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries@wisc.edu
> TaxonConcept  &  GeoSpecies Knowledge Bases
> A Semantic Web, Linked Open Data  Project
> --------------------------------------------------------------------------------------
Received on Tuesday, 21 February 2012 23:44:39 UTC

This archive was generated by hypermail 2.3.1 : Sunday, 31 March 2013 14:24:37 UTC