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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 09:50:39 -0500
Message-ID: <CAE0MQeGBGphUxL50hjXdSO48aJH9vmS5WL6oyoLvTcymyJii5A@mail.gmail.com>
To: Alan Ruttenberg <alanruttenberg@gmail.com>
Cc: Juan Sequeda <juanfederico@gmail.com>, public-lod@w3.org, Chris Mungall <cjmungall@lbl.gov>, Kingsley Idehen <kidehen@openlinksw.com>
Hi Alan,

> *We use OWL and the Virtuoso endpoint you are using doesn't understand it.
*

Isn't it more accurate to say that OBO is not the same as the OWL
standards? i.e. *OBO does not equal OWL.*

- Pete

On Wed, Feb 22, 2012 at 9:15 AM, Alan Ruttenberg
<alanruttenberg@gmail.com>wrote:

>
>
> On Wed, Feb 22, 2012 at 2:55 AM, Peter DeVries <pete.devries@gmail.com>wrote:
>
>> 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
>>
>
> Ok, I see. The problem here is the one I alluded to. We use OWL and the
> Virtuoso endpoint you are using doesn't understand it. I am ccing Kingsley
> and officially "tsk"ing him. We've known each other long enough that I'd
> have hoped he would have got some OWL religion by now. By that I don't mean
> doing full reasoning arbitrary combinations of RDF from different sources -
> but at least correctly parsing OWL is something I would have hoped be
> implemented by now.
>
> What the HAO should look like in a simple linked data browser (where some
> of the 'data' is in the form of OWL class definitions)  is something like
> this:
>
>
> http://www.ontobee.org/browser/rdf.php?o=HAO&iri=http://purl.obolibrary.org/obo/HAO_0001000
>
> Virtuoso knows how to do CBD (in fact ontobee is virtuoso as triple store
> too), but the page generator on your endpoint isn't doing it on the page it
> generates. Instead it does straight links out and links in. The links in
> are from an annotation on the axiom. It would be better there to not
> display anything, or to display a note saying there is an annotation that
> it can't display, or to properly parse the annotation (which would require
> another CBD query starting at the annotation) and display it. Kingsley, the
> source for ontobee is available - why not pick it up or use it as a spec
> for how to properly display OWL?
>
> The assertional content is:
>
> *class: tentorio-antennal muscle *
> subClassOf: antennal muscle
> subClassOf: attached_to some scape
> subClassOf: attached_to some anterior tentorial arm
>
> The SPARQL queries used to collect the content on the page are available
> by a link at the bottom of the page.
>
> The RDF that is generated can be seen by view source. I can see desirable
> improvements, e.g. adding some isDefinedBy links, and including all the
> inferrred superclasses, but that's not directly to your question, and is
> the sort of thing I mean when I say we will be working further on the RDF
> for the terms.
>
> Doing a GET for application/rdf+xml to the purl will pull in approximately
> the same RDF. The HAO folks decided to make their own browser for their
> content instead of using ontobee, which is fine. What we've tried to
> promote within the OBO community is the use of semweb technology as one
> form of dissemination, use of stable URIs as identifiers, and the ability
> to provide both human readable pages and machine readable pages. I'll get
> to Bernard's email later, but I hope you and he will realize that promoting
> and starting to successfully achieve implementation of these values for the
> OBO ontologies will yield very good value for the semantic web. There is an
> incredible amount of very well curated biological knowledge that is
> constantly being generated by that community.
>
> 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>
>>
>
> Are there what you would call character states in the example you gave
> above? I understand it as a bit of anatomy knowledge - what part connects
> to what.  I guess what I need to know is what, if any, assertions would you
> make given that you now see what was intended to be seen? Do you need a
> flattening predicate (my preference would be to use an annotation property)
> that more directly links the species concept to scape and anterior
> tentorial arm? What should it be?
>
>
>
>> And be properly interpreted on Sig.ma example http://bit.ly/zfbimy
>>
>
> I'll have to look at that later. But I would ask of it and of your
> endpoint: Is there some obligation to properly interpret what is stated
> according the web standard OWL? Surely the obligation for proper
> interpretation needs to be a mutual effort?
>
> From my point of view I want to make the OBO LOD be useful and I
> understand that there are different communities that would use it. I think
> we need to be true to the representation we choose - it provides a lot of
> benefits for query, consistency checking, etc. But we're also trying to be
> polite to others and are open to augmenting it so that it can be of utility
> to others. The key is for us to first understand how we should do that, for
> you to understand what is currently being said, and when we're done for
> your client applications to either represent what we've said too, or learn
> how to ignore it.
>
> -Alan
>
> ps. For some examples of how using OWL is yielding tangible benefits you
> could browse http://groups.google.com/group/fma-owl-2009
> In that effort I'm slowly working through translating a human anatomy
> ontology, the FMA, into OWL, and in the process discovering (and having
> fixed) thousands of errors.
>
>
>> - 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
>>
>> --------------------------------------------------------------------------------------
>>
>
>


-- 
------------------------------------------------------------------------------------
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 14:51:16 UTC

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