- From: Kingsley Idehen <kidehen@openlinksw.com>
- Date: Wed, 22 Feb 2012 13:12:57 -0500
- To: public-lod@w3.org
- Message-ID: <4F453029.7080407@openlinksw.com>
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 -- inference context applied 3. http://virtuoso.openlinksw.com/presentations/SPARQL_Tutorials/SPARQL_Tutorials_Part_5/SPARQL_Tutorials_Part_5.html#(53) > 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 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 18:13:24 UTC