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Re: How do OBO ontologies work on the LOD?

From: Kingsley Idehen <kidehen@openlinksw.com>
Date: Wed, 22 Feb 2012 15:32:22 -0500
Message-ID: <4F4550D6.4010101@openlinksw.com>
To: Peter DeVries <pete.devries@gmail.com>
CC: public-lod@w3.org
On 2/22/12 3:14 PM, Peter DeVries wrote:
> Hi Kingsley,
>
> I don't know if it is that simple, it might fix the blank nodes on my 
> endpoint.
>
> However, the OWL version of the ontology has this
>
> http://purl.org/obo/owl/HAO#HAO_0000526 URI
>
> Which shows up as in the KB http://purl.obolibrary.org/obo/HAO_0000526 
> (KB View median ocellus http://bit.ly/wOuYkf )
>
> Which resolves on the web to this 
> http://api.hymao.org/public/ontology_class/show_expanded/1779
>
> So how will this work in general on the LOD where there seems to be a 
> different set of best practices?
>
> What is the best way to add this as a schema to my endpoint?
>
> - Pete

Pete,

You can execute the following via your conductor UI or iSQL:

sparql
define get:soft "add"
INSERT INTO <http://purl.obolibrary.org/obo/hao.owl>
{?s rdfs:isDefinedBy <http://purl.obolibrary.org/obo/hao.owl> .
<http://purl.obolibrary.org/obo/hao.owl> 
<http://open.vocab.org/terms/defines> ?s.
<http://purl.obolibrary.org/obo/hao.owl> a owl:Ontology .
?s <http://www.w3.org/2007/05/powder-s#describedby> 
<http://purl.obolibrary.org/obo/hao.owl>}
FROM <http://purl.obolibrary.org/obo/hao.owl>
WHERE { optional {?s rdfs:subClassOf ?o}. optional {?s 
rdfs:subPropertyOf ?o}. optional {?s owl:equivalentClass ?o}. optional 
{?s owl:equivalentProperty ?o}. optional {?s a ?o}}
;

sparql
select distinct * from <http://purl.obolibrary.org/obo/hao.owl>  where 
{?s ?p ?o} ;

rdfs_rule_set ('hao-rule', 'http://purl.obolibrary.org/obo/hao.owl') .


Once that's done, you have a local version of the ontology that 
associated with an inference rule. After that, simply refer to the 
inference rule in your SPARQL queries via its pragma or use the &inf 
parameter re. faceted browsing URL.


Hope this helps? If not, we can move it to the Virtuoso forum and iron 
things out etc..

Kingsley
>
>
>
> On Wed, Feb 22, 2012 at 1:12 PM, Kingsley Idehen 
> <kidehen@openlinksw.com <mailto:kidehen@openlinksw.com>> wrote:
>
>     On 2/22/12 9:15 AM, Alan Ruttenberg wrote:
>>
>>
>>     On Wed, Feb 22, 2012 at 2:55 AM, Peter DeVries
>>     <pete.devries@gmail.com <mailto: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
>>         <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.
>
>     Yes, I am an OWL believer!
>
>     Pete: use the ontology in question as the basis for a Virtuoso
>     Inference rule, then invoke the describe URL with the parameter
>     for inference context application.
>
>     Example:
>
>     1.
>     http://linkeddata.uriburner.com/describe/?url=http%3A%2F%2Fpurl.org%2FNET%2Fgooglevocab%23Product
>     -- no inference context
>     2.
>     http://linkeddata.uriburner.com/describe/?uri=http%3A%2F%2Fpurl.org%2FNET%2Fgooglevocab%23Product&inf=oplweb
>     <http://linkeddata.uriburner.com/describe/?uri=http%3A%2F%2Fpurl.org%2FNET%2Fgooglevocab%23Product&inf=oplweb>
>     -- inference context applied
>     3.
>     http://virtuoso.openlinksw.com/presentations/SPARQL_Tutorials/SPARQL_Tutorials_Part_5/SPARQL_Tutorials_Part_5.html#(53)
>     <http://virtuoso.openlinksw.com/presentations/SPARQL_Tutorials/SPARQL_Tutorials_Part_5/SPARQL_Tutorials_Part_5.html#%2853%29>
>
>
>>     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
>>     <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?
>
>     Will do.
>
>
>>
>>     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.
>>
>     Yep!
>
>     SeeAlso:
>
>     1.
>     https://plus.google.com/s/inference%20owl%20linked%20data%20idehen
>     -- fuzzy search on G+ posts about virtues of OWL and Inference re.
>     data quality improvements (note: LOD cloud cache is still
>     undergoing maintenance re. LOD2 so some live demo links might not
>     work).
>
>
>>
>>         - Pete
>>
>>
>>         On Wed, Feb 22, 2012 at 12:27 AM, Alan Ruttenberg
>>         <alanruttenberg@gmail.com <mailto:alanruttenberg@gmail.com>>
>>         wrote:
>>
>>
>>
>>             On Tue, Feb 21, 2012 at 3:51 PM, Peter DeVries
>>             <pete.devries@gmail.com <mailto: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
>>             <mailto: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
>>                 <mailto: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 <http://www.juansequeda.com>
>>
>>
>>
>>                     On Mon, Feb 20, 2012 at 7:46 PM, Peter DeVries
>>                     <pete.devries@gmail.com
>>                     <mailto: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
>>                         <mailto: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 <mailto: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 <mailto: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
>>         --------------------------------------------------------------------------------------
>>
>>
>
>
>     -- 
>
>     Regards,
>
>     Kingsley Idehen	
>     Founder&  CEO
>     OpenLink Software
>     Company Web:http://www.openlinksw.com
>     Personal Weblog:http://www.openlinksw.com/blog/~kidehen  <http://www.openlinksw.com/blog/%7Ekidehen>
>     Twitter/Identi.ca handle: @kidehen
>     Google+ Profile:https://plus.google.com/112399767740508618350/about
>     LinkedIn Profile:http://www.linkedin.com/in/kidehen
>
>
>
>
>
>
>
> -- 
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries@wisc.edu <mailto: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
> --------------------------------------------------------------------------------------


-- 

Regards,

Kingsley Idehen	
Founder&  CEO
OpenLink Software
Company Web: http://www.openlinksw.com
Personal Weblog: http://www.openlinksw.com/blog/~kidehen
Twitter/Identi.ca handle: @kidehen
Google+ Profile: https://plus.google.com/112399767740508618350/about
LinkedIn Profile: http://www.linkedin.com/in/kidehen








Received on Wednesday, 22 February 2012 20:32:47 UTC

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