- From: Kingsley Idehen <kidehen@openlinksw.com>
- Date: Wed, 22 Feb 2012 15:32:22 -0500
- To: Peter DeVries <pete.devries@gmail.com>
- CC: public-lod@w3.org
- Message-ID: <4F4550D6.4010101@openlinksw.com>
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
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Received on Wednesday, 22 February 2012 20:32:47 UTC