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Re: How do OBO ontologies work on the LOD?

From: Kingsley Idehen <kidehen@openlinksw.com>
Date: Wed, 22 Feb 2012 13:12:57 -0500
Message-ID: <4F453029.7080407@openlinksw.com>
To: public-lod@w3.org
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.


-- no inference context
-- inference context applied
> 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.


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
>     --------------------------------------------------------------------------------------



Kingsley Idehen	
Founder&  CEO
OpenLink Software
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Received on Wednesday, 22 February 2012 18:13:24 UTC

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