Re: How do OBO ontologies work on the LOD?

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

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.

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 <balhoff@nescent.org> 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.
>
> 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 <pete.devries@gmail.com>
> 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 <pete.devries@gmail.com
> >
> >> 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
> >>> <alanruttenberg@gmail.com> wrote:
> >>>>
> >>>> All right, down to business.
> >>>>
> >>>> On Thu, Feb 23, 2012 at 1:32 PM, Peter DeVries <
> pete.devries@gmail.com>
> >>>> 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 <cjmungall@lbl.gov>
> >>>>> 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 <cjmungall@lbl.gov>
> >>>>>> 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
> >>>>>>> <alanruttenberg@gmail.com> wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> On Wed, Feb 22, 2012 at 2:55 AM, Peter DeVries
> >>>>>>>> <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
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> 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
> >>>>>>>>> <alanruttenberg@gmail.com> wrote:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On Tue, Feb 21, 2012 at 3:51 PM, Peter DeVries
> >>>>>>>>>> <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 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> 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
> >>>>>>>>>>>> <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
> >>>>>>>>>>>>> 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: pdevries@wisc.edu
> >>>>>>>>>>> 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: pdevries@wisc.edu
> >>>>>>>>> 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: pdevries@wisc.edu
> >>>>>>> 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: pdevries@wisc.edu
> >>>>>> 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: pdevries@wisc.edu
> >>>>> 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: pdevries@wisc.edu
> >>> 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: pdevries@wisc.edu
> >> 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: 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
--------------------------------------------------------------------------------------