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Re: How do OBO ontologies work on the LOD?

From: Bernard Vatant <bernard.vatant@mondeca.com>
Date: Wed, 22 Feb 2012 12:21:08 +0100
Message-ID: <CAK4ZFVFoEuA_ngo04HRb0hYSyYDZ8MjzFyJtva1im7W2YCQi9w@mail.gmail.com>
To: Kerstin Forsberg <kerstin.l.forsberg@gmail.com>
Cc: "public-lod@w3.org" <public-lod@w3.org>
Hi all

I've been lurking to this conversation for a while, and since Kerstin has
put my name on the table, I thought I could just drop in.

Seems to me that what Peter tries to achieve regarding linking to OBO
ontologies is a real challenge. The logic (please read : "logic" in a loose
sense here, not "formal logic", I should be cautious with such terms when
Alan are around) - underlying GeoSpecies and TaxonConcept is the LOD logic.
Linking and aggregating information is the main objective, the world is
open, so forget about global consistency of the aggregated information, use
reasoning with caution and a high level of risk, e.g., to check what is
consistent with what rather than to infer new knowledge etc. So Geospecies
reuses FOAF and SKOS and BIBO ... and refer to Geonames and DBpedia and
Freebase instances (and many more)

Actually when asked for a good example of linked data integration and
reuse, both at vocabulary and instances level, I mention Peter's work. See
[1] and [2] as illustrations.

OBO is another story. It's a linked data continent in itself, playing by
its own rules and ontological foundations, which are not necessarily the
ones of the LOD, and with no real reference to the open world outside it
(unless I miss something), even when it uses the same representation
standards (RDF and OWL).

And to answer to Kerstin's question, I wonder if the 5-star vocabulary
scales, for both data and vocabularies, apply to OBO space. And actually
I'm still pondering the introduction of OBO vocabularies in LOV, wondering
what are the pieces or modules really reused or reusable outside the OBO
space, or even if it's a good idea to consider such a thing. Are for
example OBO-in-OWL[3] or BFO[4] reusable or already used outside OBO? This
is not a provocative question, just wondering.

I appreciate Peter's willingness to bridge the gap, and if from this
conversation one could make sense of what in OBO should be reusable in LOD
and LOV, it would be great!
Best

Bernard


[1] https://plus.google.com/114406186864069390644/posts/jYfWXhA4kZu
[2] http://labs.mondeca.com/dataset/lov/details/vocabulary_geosp.html
[3] http://www.geneontology.org/formats/oboInOwl#
[4] http://www.ifomis.org/bfo/1.1

Le 22 février 2012 00:43, Kerstin Forsberg <kerstin.l.forsberg@gmail.com> a
écrit :

> 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 <http://www.taxonconcept.org/>  &  GeoSpecies<http://about.geospecies.org/> Knowledge
>>> Bases
>>> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
>>>
>>> --------------------------------------------------------------------------------------
>>>
>>
>>
>
>
> --
>
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries@wisc.edu
> TaxonConcept <http://www.taxonconcept.org/>  &  GeoSpecies<http://about.geospecies.org/> Knowledge
> Bases
> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
>
> --------------------------------------------------------------------------------------
>
>


-- 
*Bernard Vatant
*
Vocabularies & Data Engineering
Tel :  + 33 (0)9 71 48 84 59
Skype : bernard.vatant
Linked Open Vocabularies <http://labs.mondeca.com/dataset/lov>

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www.mondeca.com
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Received on Wednesday, 22 February 2012 11:22:07 UTC

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