[tdwg-content] More Strange Monkey Business-like things in GBIF KOS Document

Hilmar Lapp hlapp at nescent.org
Thu Feb 17 22:32:29 CET 2011

On Feb 17, 2011, at 3:23 PM, Shawn Bowers wrote:

> Both OBOE and EQ do introduce classes that prescribe how to  
> structure new classes and type
> individuals

That's actually not quite true. The EQ model itself doesn't prescribe  
any new classes or the types that individuals must be of; instead it  
simply says that a phenotype instance can be expressed as some  
instance of a quality Q that inheres_in some instance of an entity E,  
and thus a class of phenotypes (or observations of an organism's  
characteristics) is the intersection of all instances of Q (a subclass  
restriction), and all things that inhere_in E (a property restriction).

While typically we will draw Q and E from certain ontologies (such as  
PATO for qualities), you can designate any class (term) in those  
places, and the class expression by itself will not support inferences  
about the nature of Q or E or their instances (the ontologies that Q  
and E are drawn from do that). The class expression itself is often  
anonymous, but there are (so-called "pre-composed") ontologies that  
identify and label them.

That being said, while EQ in principle allows you to do real crazy  
things if you want to (which perhaps is what Joel means by schema- 
last?), if you want to be able to do discovery and reasoning with a  
set of EQ class expressions from different sources, they will need to  
follow some shared conventions, such as not simply making up quality  
and entity terms as needed, but drawing them from PATO and shared  
entity ontologies.

Conversely, OBOE does prescribe the nature of the things that it  
relates to each other in the model, the cardinality of those  
relationships, and what it means for an instance it is has such a  
relationship. For example, if I assert o oboe:ofEntity e, the  
semantics of oboe:ofEntity prescribe that o is an instance of  
oboe:Observation, e is an instance of oboe:Entity, and if I also  
assert o oboe:ofEntity e1, it prescribes that e and e1 are identical,  
i.e., the same instance.

I think these differences are a result of how they were motivated, and  
it is interesting to me that Joel would pick these as examples for  
illustrating "schema-lastishness". OBOE was motivated by having a  
unified data model for observational data, in the interest of better  
data exchange and integration. I think all its class and property  
constraints are a reflection of that - there is a desire not to "allow  
anything". Conversely, EQ wouldn't make for a good model in which to  
exchange arbitrary observational data - there would be no guarantees  
for what you get. However, it is very powerful for reasoning over the  
semantics of the observations (see the Washington et al 2009 paper),  
which is what it was conceived for.

On Thu, Feb 17, 2011 at 11:28 AM, joel sachs <jsachs at csee.umbc.edu>  
> Do you (or does anyone else on the list) know the status of OBD?  
> From the

Funny you should ask. We're in the final stages of writing up a  
manuscript about it. I can share a preprint with you next week. OBD is  
what is underpinning the Phenoscape Knowledgebase (http://kb.phenoscape.org 

The URL is http://www.berkeleybop.org/obd/. It is still pretty  
outdated, but will be updated very soon.

> Is it still the plan to integrate OBD into BioPortal?

I don't think so. And there are lots of resources working on that (at  
least in the biomedical domain), so it'd be hard for them to pick what  
to follow.

> So in the OBOE case, the characteristics (color, perimeter texture,  
> basic shape) are given a priori, while in the EQ case they would  
> (presumably) be abstracted during subsequent ontology development.

Yes. They are implied by the subclass structure of PATO (and thus  
subject to change).

> it might be worth experimenting with tag-driven ontology evolution,  
> as in [1], where tags are associated to concepts in an ontology.  
> [...] So the domain expert/knowledge engineer
> partnership is preserved, but with the domain expert role being  
> replaced by collective wisdom from the community.

Are you aware of the "Fast, Cheap, and Out of Control" paper from Mark  
Wilkinson's group:
Good et al. 2006. Fast, Cheap and Out of Control: A Zero Curation  
Model for Ontology Development. Pacific Symposium on Biocomputing 11:  


: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :

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