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Re: How do OBO ontologies work on the LOD?

From: Peter DeVries <pete.devries@gmail.com>
Date: Thu, 23 Feb 2012 13:32:15 -0500
Message-ID: <CAE0MQeGVgd-b2tT2f2q6U5qPpmjwxWUv78Pvycs4xkZ42jCMrA@mail.gmail.com>
To: Chris Mungall <cjmungall@lbl.gov>
Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, Juan Sequeda <juanfederico@gmail.com>, public-lod@w3.org, Kingsley Idehen <kidehen@openlinksw.com>, andy_deans@ncsu.edu, Matt Yoder <diapriid@gmail.com>, Nathan Wilson <nwilson@eol.org>, David Patterson <dpatterson@mbl.edu>, Anne Thessen <athessen@mbl.edu>
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

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

Mapped URI http://purl.obolibrary.org/obo/HAO_0000000

HTML Page http://api.hymao.org/public/ontology_class/show_expanded/4048

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.

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.

(The assumption being that most of the use of these vocabularies will be in
relationship to LOD URI's)

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.

Does this help clarify my concern?

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 <http://www.taxonconcept.org/>  &  GeoSpecies<http://about.geospecies.org/> Knowledge
>>>>>>>> Bases
>>>>>>>> A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
>>>>>>>>
>>>>>>>> --------------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>>> ------------------------------------------------------------------------------------
>>>>>> 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
>>>>>>
>>>>>> --------------------------------------------------------------------------------------
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> ------------------------------------------------------------------------------------
>>>> 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
>>>>
>>>> --------------------------------------------------------------------------------------
>>>>
>>>
>>>
>>
>>
>> --
>>
>> ------------------------------------------------------------------------------------
>> 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
>>
>> --------------------------------------------------------------------------------------
>>
>>
>>
>
>
> --
>
> ------------------------------------------------------------------------------------
> 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
>
> --------------------------------------------------------------------------------------
>
>
>


-- 
------------------------------------------------------------------------------------
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
--------------------------------------------------------------------------------------
Received on Thursday, 23 February 2012 18:32:44 UTC

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