Survey of modular ontology techniques and their applications in the biomedical domain

[Gary Berg-Cross <gbergcross@xxxxxxxxx>]

Leo,

>The given example is very simple, and for real application, would need  (points)1-4 (in Leo's email) to help assure us that >the equivalences are accurate.

I would further note that the illustrations of ontology integration you provided were responsive to my original focus frame of Owl Imports - so at the language level.  But as we consider what can be done with the language we quickly get into discussion of whether this is appropriate for the underly content's concepts and their relations being represented.  While we can point to documentation in the ontologies themselves we might be dealing with 2 or more ontologies representing concepts in data and thus look to the conceptual models for DBs holding that data.

The point here is that in practice we may be reusing the content of conceptual and logical models and their documentation as well as reusing ontologies and documentation.  This may be particularly true when Big Data meets Ontologies and we look at ways of them working together.

This is a point that john Sowa might support in part and he is scheduled to be a speaker at the 2nd Track A session on Content Reuse, so perhaps we will hear relevant things in his talk.

Gary Berg-Cross, Ph.D.  

gbergcross@xxxxxxxxx     

http://ontolog.cim3.net/cgi-bin/wiki.pl?GaryBergCross

NSF INTEROP Project  

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SOCoP Executive Secretary

Knowledge Strategies    

Potomac, MD

240-426-0770

On Fri, Feb 7, 2014 at 4:03 PM, Obrst, Leo J. <lobrst@xxxxxxxxx> wrote:

Gary,

 

Yes, indeed. Really the ontologies require more documentation:

1) Definitions of what the classes/properties mean in standard natural language (English, etc.)

2) If available, more strict axiomizations: in OWL ontologies, if the axioms exceed OWL expressivity, one can express these in textual annotations.

3) The use cases (pragmatics) for classes/properties/axioms, at least expressed in ontology-general or more specific textual annotations.

 

Other:

4) Are instances available, and can we compare them against their specific (1-3) documentation?

 

The given example is very simple, and for real application, would need 1-4 to help assure us that the equivalences are accurate.

 

Thanks,

Leo

 

 

From: ontology-summit-bounces@xxxxxxxxxxxxxxxx [mailto:ontology-summit-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Gary Berg-Cross
Sent: Friday, February 07, 2014 3:34 PM

To: Ontology Summit 2014 discussion
Subject: Re: [ontology-summit] OWl and Knowledge reuse via import and modularization

 

Leo

 

Thank you for advancing the conversation.  Concrete, illustrative examples can help focus the discussion. And you've shown how to do it if the concepts are equivalent or thought so.

 

In your examples things are a bit simple and would be a bit more difficult, I think, with ontologies that were generated without considering what had been done in a domain.  So for example equating/equivalence between A and B ontologies seems directly possible, but if one of them was a bit more precise and detailed and said that PLACE hasA LOCATION then we might not equate PLACE in A with LOCATION  in B. 

We'd know more about what is meant by the 2 concepts if we looked at the data instances they represent and found that in A we have place locations like Grand Canyon  and in B they are lat-lon. 

Gary Berg-Cross, Ph.D.  

gbergcross@xxxxxxxxx     

http://ontolog.cim3.net/cgi-bin/wiki.pl?GaryBergCross

NSF INTEROP Project  

http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0955816

SOCoP Executive Secretary

Knowledge Strategies    

Potomac, MD

240-426-0770

 

On Fri, Feb 7, 2014 at 3:05 PM, Obrst, Leo J. <lobrst@xxxxxxxxx> wrote:

Folks,

 

I quickly created 3 ontologies that illustrate an integration ontology pattern:

 

Integration-a-b.owl imports both ontology-a.owl and ontology-b.owl. Then in integration-a-b.owl various equivalences are made.

 

Integration-a-b-ontology-imports.png shows the imports.

Ontology-a-classes.png shows the classes of ontology-a.owl.

Ontology-b-classes.png shows the classes of ontology-b.owl.

Classes-equivalences-integration-a-b-ontology.png shows the classes and equivalences of integration-a-b.owl.

 

The equivalences are shown as darker ovals in the last png file above.

 

I hope this is a helpful illustration of one very typical pattern.

 

Thanks,

Leo

 

 

From: ontology-summit-bounces@xxxxxxxxxxxxxxxx [mailto:ontology-summit-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Andrea Westerinen
Sent: Tuesday, February 04, 2014 10:33 PM
To: Ontology Summit 2014 discussion

Subject: Re: [ontology-summit] OWl and Knowledge reuse via import and modularization

 

Gary, I emailed on this topic (importing everything versus modularity) a few weeks ago on another Summit thread (and Leo expanded on it).  Also, I just posted about it on my blog.  Here is the text:

 

[My previous post talked ...] about creating small, focused "modules" of cohesive semantic content.  And, since these modules have to be small, they can't (and shouldn't) completely define everything that might be referenced.  Some concepts will be under-specified.  

So, how we tie the modules together in an application?

In a recent project, I used the equivalentClass OWL semantic to do this. For example, in a Person ontology, I defined the Person concept with its relevant properties.  When it came to the Person's Location - that was just an under-specified (i.e., empty) Location class.  I then found a Location ontology, developed by another group, and opted to use that.  Lastly, I defined an "integrating" ontology that imported the Person and Location ontologies, and specified an equivalence between the relevant concepts.  So, PersonNamespace:Location was defined as an equivalentClass to LocationNamespace:Location. Obviously, the application covered up all this for the users, and my triple store (with reasoner) handled the rest.

This approach left me with a lot of flexibility for reuse and ontology evolution, and didn't force imports except in my "integrating" ontology.  And, a different application could bring in its own definition of Location and create its own "integrating" ontology.

But, what happens if you can't find a Location ontology that does everything that you need?  You can still integrate/reuse other work, perhaps defined in your integrating ontology as subclasses of the (under-specified) PersonNamespace:Location concept.

 

This approach also works well when developing and reusing ontologies across groups.  Different groups may use different names for the same semantic, may need to expand on some concept, or want to incorporate different semantics.  If you have a monolithic ontology, these differences will be impossible to overcome.  But, if you can say things like  "my concept X is equivalent to your concept Y" or "my concept X is a kind of your Y with some additional restrictions" - that is very valuable.  Now you get reuse instead of redefinition.

 

 

Andrea

On Tue, Feb 4, 2014 at 2:34 PM, Gary Berg-Cross <gbergcross@xxxxxxxxx> wrote:

OWL provides an owl:imports construct that allows people to combine ontologies by including all the axioms contained in an external ontology in one’s local ontology. But then , everything in the transitive closure of the imported ontology becomes a part of the local ontology. Have people found this to be a problem for their work and if so what are best practices around it?

 

There seem to be a number of efforts to get around this,such as modular approaches  but I'm not sure what the experience has been with them.The 

Survey of modular ontology techniques and their applications in the biomedical domain
by

Jyotishman Pathak,* Thomas M. Johnson, and Christopher G. Chute has some discussion.

Survey of modular ontology techniques and their applications in the biomedical domain

Jie Bao, Giora Slutzki and Vasant Honavar proposed a modular ontology language to get around 

http://www.aaai.org/Papers/AAAI/2007/AAAI07-206.pdf

 

Perhaps others have some experience with what these discuss.

 

Gary Berg-Cross, Ph.D.  

gbergcross@xxxxxxxxx     

http://ontolog.cim3.net/cgi-bin/wiki.pl?GaryBergCross

NSF INTEROP Project  

http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0955816

SOCoP Executive Secretary

Knowledge Strategies    

Potomac, MD

240-426-0770

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Andrea Westerinen

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