On Feb 24, 2012, at 1:40 PM, Peter DeVries wrote: > Hi Guys, > > Since you are working with Ruby you might want to check out the work of the > ruby-rdf group, > > In my experience they do really good work, > > RDF.rb: Linked Data for Ruby > http://rdf.rubyforge.org/ > https://github.com/bendiken/rdf > > Arto Bendiken - http://ar.to/ > Ben Lavender - http://bhuga.net/ > Gregg Kellogg - http://kellogg-assoc.com/ > > bendiken (Arto Bendiken) > https://github.com/bendiken > > gkellogg (Gregg Kellogg) > https://github.com/gkellogg
Mine is the active fork for most of the tools, including http://github.com/gkellogg/rdf. The latest up-to-date versions are running online through a simple app at http://rdf.greggkellogg.net, which includes comprehensive documentation for all the appropriate gems. > bhuga (Ben Lavender) > https://github.com/bhuga > > They have a mailing list > http://lists.w3.org/Archives/Public/public-rdf-ruby/ > > For the future of your project and perhaps others you might want to consider > using RDFa in the html pages, then you would not have to worry about creating > an .rdf view. > * I am not sure if RDFa pages are completely understood yet by all the > related tools and I think that there are still some standardisation going on. The rdf-rdfa gem is pretty much the most up-to-date implementation anywhere. The spec is heading to Candiate Release, so it is pretty stable now. I'll have an update in the next week that gets it fully up-to-date with the CR version of the spec. The rdf-rdfa gem also includes an HTML writer, for which you can provide a Haml template to get pretty flexible output from an arbitrary RDF graph in HTML+RDFa. The toolset (through the linkeddata gem, which bundles RDF.rb and most of the other readers and writers) includes pretty much every common RDF format. (more below). Gregg > Also Andy Deans had suggested that we might want to have a separate meeting > about these issues in the near future, > > I will be in Woods Hole working with the Eol,org and GlobalNames,org at least > until the end of March. > > Respectfully, > > - Pete > > On Fri, Feb 24, 2012 at 10:38 AM, Jim Balhoff <[email protected]> wrote: > I tried this: > > curl -H "Accept:application/rdf+xml" -L > 'http://purl.obolibrary.org/obo/HAO_0000144' > > and for some reason absolutely nothing is returned. We will need to fix some > problems with our Accept handling in Rails. I thought that checking for xml > would subsume rdf+xml, but apparently not. The sinatra-linked data gem (or sparql gem, which includes sinatra-sparql) may be useful in performing content negotiation to provide a variety of formats. > Thanks, > Jim > > On Feb 24, 2012, at 10:29 AM, Matt wrote: > > > Hi Pete, > > > > Please keep myself and, more importantly Jim (who did the hard work > > setting things up here) in the loop on these issues. I didn't see > > anything going on here until the discussion had gone on for some time- > > there is a very good chance we could have prevented some confusion for > > Alan etc. > > > > Jim asked me to pass on the message below. > > > > Thanks, > > Matt > > > > --- > > > > Please forward this to everybody: > > > > curl -H "Accept:application/xml" -L > > 'http://purl.obolibrary.org/obo/HAO_0000144' > > > > does return RDF from Ontobee. If there is a way we should be handling > > the Accept header better then please let us know. > > > > Thanks, > > Jim > > > > --- > > > > On Fri, Feb 24, 2012 at 12:37 AM, Peter DeVries <[email protected]> > > wrote: > >> Hi Alan, > >> > >> I think I have figured out what was happening. > >> > >> This page should point to the obolibrary version of the > >> ontology http://obofoundry.org/cgi-bin/detail.cgi?id=hymenoptera_anatomy > >> > >> Also Google Chrome interprets the obolibrary owl files below as being a RSS > >> feed which suggests that the server might not have the correct mime type > >> setting. > >> > >> http://purl.obolibrary.org/obo/hao.owl > >> > >> The Vapour Validator and Sindice issues still exit with URI's > >> like http://purl.obolibrary.org/obo/HAO_0000148 , but I see why we were > >> disagreeing :-) > >> > >> In summary: > >> > >> All the previous OBO ontologies that had URI's like > >> this http://purl.org/obo/owl/HAO#HAO_0001313 > >> > >> Now have obolibrary URI's like > >> this http://purl.obolibrary.org/obo/HAO_0001313 > >> > >> Which means that the Vapour and Sindice issues are not with OBO URI's in > >> general but with how each ontology deals with these requests. > >> > >> Since the request for rdf ("Accept: application/rdf+xml") is sent to the > >> obolibrary server should it do the redirection to something like? > >> > >> http://api.hymao.org/public/ontology_class/show_expanded/7563.rdf > >> > >> I am sorry for the misunderstanding but I referenced where I got the > >> ontology I was using back in message 7 of this thread. > >> > >> Hi Alan, > >> > >> Here is an example from the Hymenoptera Anatomy Ontology > >> > >> http://obofoundry.org/cgi-bin/detail.cgi?id=hymenoptera_anatomy .... > >> > >> > >> Following LOD best practices is needed so services like Sig.ma can figure > >> out how to correctly interpret LOD triples and display them like this. > >> > >> http://sig.ma/search?pid=f1e537693d3d272556a8ca439ca021d9 > >> > >> - Pete > >> > >> > >> > >> > >> On Thu, Feb 23, 2012 at 10:23 PM, Peter DeVries <[email protected]> > >> wrote: > >>> > >>> 1) > >>> > >>>> in a big deal about LOD versus OWL. > >>> > >>> Arrggh! It is OBO that is not OWL > >>> > >>> What is the extension that is used for an OBO file? .owl? No it is .obo > >>> > >>> OBO format hymenoptera_anatomy.obo > >>> > >>> Is this one of the OWL syntaxes or it's own syntax? > >>> > >>> [Term] > >>> id: HAO:0000000 > >>> name: anatomical entity > >>> def: "Biological entity that is either an individual member of a > >>> biological species or constitutes the structural organization of an > >>> individual member of a biological species." [ISBN:978-1-84628-88] > >>> xref: CARO:0000000 > >>> > >>> Doesn't the obo syntax need to be translated into OWL? > >>> > >>> It is important to note that several other widely used biology ontologies > >>> are in one of the actual OWL syntaxes and follow LOD best practices. > >>> > >>> For instance http://purl.uniprot.org/core/ > >>> > >>> > >>> It is more than just a problem with the HAO ontology, a Mosquito ontology > >>> URI also fails when I tried it on Vapour and Sindice. > >>> > >>> > >>> Why is it so important to portray OBO ontologies as following LOD best > >>> practices when they clearly do not? > >>> > >>> They do not behave as expected by Tim Berners-Lee's 4 > >>> rules http://www.w3.org/DesignIssues/LinkedData.html > >>> > >>> When I look in the ontology, I see this > >>> URI http://purl.org/obo/owl/HAO#HAO_0001313 > >>> > >>> Where in this ontology is there anything that relates the URI above to the > >>> URI below? > >>> > >>> http://purl.obolibrary.org/obo/HAO_0001313 (the one displayed on the web > >>> site) > >>> > >>> I am done, it think it is pretty clear that the OBO URI's work differently > >>> than the LOD URI's. > >>> > >>> - Pete > >>> > >>> > >>> On Thu, Feb 23, 2012 at 8:38 PM, Alan Ruttenberg > >>> <[email protected]> wrote: > >>>> > >>>> All right, down to business. > >>>> > >>>> On Thu, Feb 23, 2012 at 1:32 PM, Peter DeVries <[email protected]> > >>>> wrote: > >>>>> > >>>>> Hi Chris, > >>>>> > >>>>>> 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 > >>>>> > >>>>> As it is implemented HAO does not follow best practices as described > >>>>> here: > >>>>> > >>>>> http://www.w3.org/DesignIssues/LinkedData.html > >>>>> > >>>>> ( Additional Information > >>>>> Here http://linkeddata.org/guides-and-tutorials ) > >>>>> > >>>>> Specifically the rule #3 When someone looks up a URI, provide useful > >>>>> information, using the standards (RDF*, SPARQL) > >>>>> > >>>>> You can test this by running curl commands like > >>>>> > >>>>> curl -H "Accept: application/rdf+xml" > >>>>> http://purl.obolibrary.org/obo/HAO_0000000 > >>>> > >>>> > >>>> I get > >>>> <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> > >>>> <HTML> > >>>> <HEAD> > >>>> <TITLE>302 Found</TITLE> > >>>> </HEAD> > >>>> <BODY> > >>>> <H1>Found</H1> > >>>> The resource requested is available <A > >>>> HREF="http://www.berkeleybop.org/ontologies/HAO_0000000";>here</A>.<P> > >>>> </BODY> > >>>> </HTML> > >>>> > >>>> Curl is not following the redirects. With wget it does, but there is > >>>> still a problem: > >>>> > >>>> wget --header "Accept: application/rdf+xml" > >>>> http://purl.obolibrary.org/obo/HAO_000000 > >>>> --2012-02-23 20:26:02-- http://purl.obolibrary.org/obo/HAO_000000 > >>>> Resolving purl.obolibrary.org (purl.obolibrary.org)... 132.174.1.35 > >>>> Connecting to purl.obolibrary.org > >>>> (purl.obolibrary.org)|132.174.1.35|:80... connected. > >>>> HTTP request sent, awaiting response... 302 Moved Temporarily > >>>> Location: http://www.berkeleybop.org/ontologies/HAO_000000 [following] > >>>> --2012-02-23 20:26:02-- http://www.berkeleybop.org/ontologies/HAO_000000 > >>>> Resolving www.berkeleybop.org (www.berkeleybop.org)... 131.243.192.99 > >>>> Connecting to www.berkeleybop.org > >>>> (www.berkeleybop.org)|131.243.192.99|:80... connected. > >>>> HTTP request sent, awaiting response... 303 See Other > >>>> Location: http://purl.obolibrary.org/obo/HAO/about/HAO_000000 [following] > >>>> --2012-02-23 20:26:03-- > >>>> http://purl.obolibrary.org/obo/HAO/about/HAO_000000 > >>>> Connecting to purl.obolibrary.org > >>>> (purl.obolibrary.org)|132.174.1.35|:80... connected. > >>>> HTTP request sent, awaiting response... 302 Moved Temporarily > >>>> Location: http://api.hymao.org/api/ontology/ontology_class/HAO_000000 > >>>> [following] > >>>> --2012-02-23 20:26:03-- > >>>> http://api.hymao.org/api/ontology/ontology_class/HAO_000000 > >>>> Resolving api.hymao.org (api.hymao.org)... 128.194.196.117 > >>>> Connecting to api.hymao.org (api.hymao.org)|128.194.196.117|:80... > >>>> connected. > >>>> HTTP request sent, awaiting response... 404 Not Found > >>>> 2012-02-23 20:26:04 ERROR 404: Not Found. > >>>> > >>>> The multiple redirects are fine - an artifact of the fact that purl's > >>>> redirect rules are not expressive enough. But in the end we don't get > >>>> RDF, > >>>> which we should, so this is indeed a problem that I'll take up with the > >>>> HAO > >>>> developers. They chose to handle the PURLs themselves rather than using > >>>> ontobee, and I had the understanding that they would do the RDF bit too > >>>> but > >>>> something is amiss. > >>>> > >>>> > >>>> However, I think testing using the Vapour Validator is easier to > >>>> understand. > >>>>> > >>>>> > >>>>> This might best be shown in comparison to a LOD OWL class that works > >>>>> correctly, > >>>>> > >>>>> OBO Ontology URI http://purl.org/obo/owl/HAO#HAO_0000000 > >>>> > >>>> > >>>> This is a legacy URI. The OBO to OWL translation is undergoing a > >>>> disruptive change so that we can deliver a page per term. I'm not sure > >>>> where > >>>> you got this URI from. HAO is distributed at > >>>> http://purl.obolibrary.org/obo/hao.owl and I see there only the URI > >>>> below. > >>>> > >>>>> > >>>>> Mapped URI http://purl.obolibrary.org/obo/HAO_0000000 > >>>> > >>>> > >>>> Mapped by who? > >>>> > >>>>> > >>>>> HTML Page http://api.hymao.org/public/ontology_class/show_expanded/4048 > >>>> > >>>> > >>>> Yes. Now if they followed the protocol that we suggested that page would > >>>> have page source that is RDF/XML and show html in the browser. I'll ask > >>>> them > >>>> about this. Understand that there isn't a boss of OBO, and that the > >>>> developers had and exercised the choice to have the PURLs redirect to > >>>> their > >>>> site. However I believe they want to serve RDF so I'll find out what's > >>>> up. > >>>> > >>>>> > >>>>> > >>>>> Check in the Vapour Validator http://validator.linkeddata.org/vapour > >>>>> > >>>>> For comparison > >>>>> > >>>>> URI for the Species Apis mellifera > >>>>> http://lod.taxonconcept.org/ses/z9oqP#Species > >>>>> > >>>>> Human Page http://lod.taxonconcept.org/ses/z9oqP.html > >>>>> > >>>>> Check the URI using the Vapour Validator > >>>>> > >>>>> It is my opinion that this ontology could have been (and could still be > >>>>> modified to) implemented in a way that followed LOD best practices. > >>>> > >>>> > >>>> Yes, and it will be modified to provide RDF as I have said. > >>>> > >>>>> > >>>>> > >>>>> My concern is that other groups like the beetle people > >>>>> (Coleopterologists) etc. would see the HAO ontology and assume that they > >>>>> should also use OBO. > >>>> > >>>> > >>>> They should ;-) > >>>> > >>>>> > >>>>> (The assumption being that most of the use of these vocabularies will be > >>>>> in relationship to LOD URI's) > >>>> > >>>> > >>>> I still don't know what a LOD URI is. A URI is a URI. > >>>> > >>>>> > >>>>> In other words, if the HAO ontology followed LOD best practices then it > >>>>> would be a good project to model similar efforts on - but it does not. > >>>> > >>>> > >>>> You are reading too much into the situation. Either there's a > >>>> misconfiguration or they haven't implemented yet. Simple as that. > >>>> > >>>>> > >>>>> Does this help clarify my concern? > >>>> > >>>> > >>>> Well, it was a long way round, but I hadn't realized they weren't serving > >>>> RDF. Note for future - don't get wrapped up (an get me wrapped up ;-) in > >>>> a > >>>> big deal about LOD versus OWL. A request to that URI isn't behaving as > >>>> expected. It can be fixed. It will be fixed. Expect something similar to > >>>> the > >>>> RDF at > >>>> http://www.ontobee.org/browser/rdf.php?o=HAO&iri=http://purl.obolibrary.org/obo/HAO_0000000 > >>>> > >>>> I'll follow up privately with the HAO developers cc you. > >>>> > >>>> Later, > >>>> Alan > >>>> > >>>>> > >>>>> > >>>>> Respectfully, > >>>>> > >>>>> - Pete > >>>>> > >>>>> > >>>>> On Thu, Feb 23, 2012 at 10:09 AM, Chris Mungall <[email protected]> > >>>>> wrote: > >>>>>> > >>>>>> > >>>>>> 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 > >>>>>> > >>>>>> -------------------------------------------------------------------------------------- > >>>>>> > >>>>>> > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> > >>>>> ------------------------------------------------------------------------------------ > >>>>> 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 > >> -------------------------------------------------------------------------------------- > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > > > > > -- > ------------------------------------------------------------------------------------ > 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 > --------------------------------------------------------------------------------------
