On Feb 23, 2012, at 9:40 AM, Peter DeVries wrote: > Hi Chris, > > http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#5 > > "On completions this section will define the semantics of the entirety of OBO > via mappings to OWL2. The mappings could also be used to specify a > translation procedure and/or an interface to OWL tools (such as OWL > reasoners). > > The translation is defined using a translation function T which translates (a > fragment of) OBO into OWL DL. The definition of T is often recursive, but it > will eventually "ground out" in (a fragment of) OWL DL." > > The fact that OBO can be mapped to a subset of OWL 2 LD is not the same as > saying it is OWL 2.
Yes - OBO Format has a formal semantics that is a subset of OWL2-DL > In any case this is not really relevant, since it does not address my main > concern. > > That OBO and the OBO ontologies converted to OWL (specifically the > hymenoptera ontology) do not follow LOD best practices. I'm not aware of the issue - what should we do to improve this? > If there is no intention of using this ontology for LOD applications then > this is not a problem. > > Should I interpret your comment as supporting the idea that those interested > in creating applications for the LOD should do so by creating new OBO > ontologies when they could just as easily create new OWL ontologies that > follow LOD best practices? They could do this, the question of whether they should do this is highly dependent on the ontology they're creating. But in general I think most people developing a new ontology should use an OWL syntax for the primary representation. > If you look at how this project was setup, it seems to me that it would have > been much more direct and LOD compliant to base their URI's and ontology on > URI's > related to URL's like this > http://api.hymao.org/projects/32/public/ontology_class/show/1033 > > Than to a non LOD OBO URI? Sorry, I'm not following. In OBO format you can map OBO-Style IDs to any URI scheme you like. The default is to map to a http://purl.obolibrary.org/obo URI > Respectfully, > > - Pete > > On Wed, Feb 22, 2012 at 3:48 PM, Chris Mungall <[email protected]> wrote: > > 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 >> -------------------------------------------------------------------------------------- > > > > > -- > ------------------------------------------------------------------------------------ > 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 > --------------------------------------------------------------------------------------
