W3C home > Mailing lists > Public > public-lod@w3.org > February 2012

Re: How do OBO ontologies work on the LOD?

From: Gregg Kellogg <gregg@kellogg-assoc.com>
Date: Fri, 24 Feb 2012 20:21:38 -0500
To: Peter DeVries <pete.devries@gmail.com>
CC: Jim Balhoff <balhoff@nescent.org>, Matt <diapriid@gmail.com>, Alan Ruttenberg <alanruttenberg@gmail.com>, Chris Mungall <cjmungall@lbl.gov>, Juan Sequeda <juanfederico@gmail.com>, "public-lod@w3.org" <public-lod@w3.org>, Kingsley Idehen <kidehen@openlinksw.com>, "andy_deans@ncsu.edu" <andy_deans@ncsu.edu>, Nathan Wilson <nwilson@eol.org>, David Patterson <dpatterson@mbl.edu>, Anne Thessen <athessen@mbl.edu>, Gregg Kellogg <gregg@kellogg-assoc.com>
Message-ID: <A7FC9A0F-EC00-40AA-8E13-B175B9A1A3A0@greggkellogg.net>
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 <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.

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 <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  &  GeoSpecies Knowledge Bases
> A Semantic Web, Linked Open Data  Project
> --------------------------------------------------------------------------------------
Received on Saturday, 25 February 2012 01:22:24 UTC

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