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Re: How do OBO ontologies work on the LOD?

From: Peter DeVries <pete.devries@gmail.com>
Date: Wed, 22 Feb 2012 02:55:42 -0500
Message-ID: <CAE0MQeFHP0aqm8JbBL47+JoVXUPooZUjnRDQd0eN7_GOSDVPfA@mail.gmail.com>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
Cc: Juan Sequeda <juanfederico@gmail.com>, public-lod@w3.org, Chris Mungall <cjmungall@lbl.gov>
Hi Alan,

Here is an example from the Hymenoptera Anatomy Ontology

http://obofoundry.org/cgi-bin/detail.cgi?id=hymenoptera_anatomy

Example via my endpoint
http://lsd.taxonconcept.org/describe/?url=http://purl.obolibrary.org/obo/HAO_0001000&sid=1151

I was thinking that the character states described in this ontology could
be attached to species like this.

<http://lod.taxonconcept.org/ses/z9oqP#Species> <somePredicate>
<someHAOCharacterState>

And be properly interpreted on Sig.ma example http://bit.ly/zfbimy

- Pete

On Wed, Feb 22, 2012 at 12:27 AM, Alan Ruttenberg
<alanruttenberg@gmail.com>wrote:

>
>
> On Tue, Feb 21, 2012 at 3:51 PM, Peter DeVries <pete.devries@gmail.com>wrote:
>
>> 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.
>>
>
> Which one?
>
>
>>
>> In this particular use case I was thinking of applying the terms and
>> properties described by the ontology to my species concepts.
>>
>
> This is a nice example and should be supported. An immediate suggestion is
> to send mail to  obo-discuss@lists.sourceforge.net as that is where you
> will find both the developers of the OBO LOD support as well as the
> biologist community.
>
>
>>
>> For instance:
>>
>> species X has this metabolic pathway.  (which would be useful for finding
>> species with potential drug interactions or other chemical reactions)
>>
>
> We're in the process of revising BFO and the relations ontology. A draft
> version is at http://purl.obolibrary.org/obo/bfo.owl
>
> In terms of that, your statement might be represented as
>
> <species> subclassOf 'has site of' some <metabolic process>
> if you want to represent that all members of the species have the process
>
> or
>
> <anonymous instance of species> 'has site of'  <anonymous instance of
> process>
>
> e.g.
>
> @prefix obo: <http://purl.obolibrary.org/obo/>
> @prefix hasSiteOf: <http://purl.obolibrary.org/obo/BFO_0000067>
>
> _:a rdf:type <species>
> _:b rdf:type <metabolic process>
> _:a hasSiteOf: _:b
>
> If you want to represent that the process happens in some individuals of
> this species.
>
> In the above I write <species> where you would write the uri of your
> species class (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9903) , and
> <metabolic process> where you would write the uri of your process class
> (e.g. http://purl.obolibrary.org/obo/GO_0030245).
>
>
>
>> 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.
>>
>
> Not sure what you mean by this.
>
>
>>
>> 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
>>
>
> Example?
>
>> .
>> 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.
>>
>
> Examples would be helpful. But note that it is our intention that we *do*
> play well on the LOD cloud. However also note, we work in OWL and much of
> what we say is about types/classes, and many(most?) linked data browsers
> don't understand or present OWL in a meaninful way. One of the reasons we
> have developed ontobee is that it is designed to do justice to linked
> ontology terms that are defined in terms of OWL. So class expressions are
> not left as messes of bnodes, but instead parsed and displayed as OWL. I'd
> like to see more linked data browsers do the same.
>
>
>> Does my interpretation seem appropriate to you or am I missing something?
>>
>
> I hope you are missing something :) But please elaborate so we can see.
>
>
>>
>> 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
>>
>> --------------------------------------------------------------------------------------
>>
>
>


-- 
------------------------------------------------------------------------------------
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
--------------------------------------------------------------------------------------
Received on Wednesday, 22 February 2012 07:56:15 UTC

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