OBO-Format is a subset of OWL2-DL http://oboformat.org
Cheers Chris On Feb 22, 2012, at 9:50 AM, Peter DeVries wrote: > 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 <[email protected]> > wrote: > > > On Wed, Feb 22, 2012 at 2:55 AM, Peter DeVries <[email protected]> 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 <[email protected]> > wrote: > > > On Tue, Feb 21, 2012 at 3:51 PM, Peter DeVries <[email protected]> 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 [email protected] 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 <[email protected]> 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 <[email protected]> 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: [email protected] > TaxonConcept & GeoSpecies Knowledge Bases > A Semantic Web, Linked Open Data Project > -------------------------------------------------------------------------------------- > > > > > -- > ------------------------------------------------------------------------------------ > Pete DeVries > Department of Entomology > University of Wisconsin - Madison > 445 Russell Laboratories > 1630 Linden Drive > Madison, WI 53706 > Email: [email protected] > TaxonConcept & GeoSpecies Knowledge Bases > A Semantic Web, Linked Open Data Project > -------------------------------------------------------------------------------------- > > > > > -- > ------------------------------------------------------------------------------------ > Pete DeVries > Department of Entomology > University of Wisconsin - Madison > 445 Russell Laboratories > 1630 Linden Drive > Madison, WI 53706 > Email: [email protected] > TaxonConcept & GeoSpecies Knowledge Bases > A Semantic Web, Linked Open Data Project > -------------------------------------------------------------------------------------- > > > > > -- > ------------------------------------------------------------------------------------ > Pete DeVries > Department of Entomology > University of Wisconsin - Madison > 445 Russell Laboratories > 1630 Linden Drive > Madison, WI 53706 > Email: [email protected] > TaxonConcept & GeoSpecies Knowledge Bases > A Semantic Web, Linked Open Data Project > --------------------------------------------------------------------------------------
