[tdwg-content] More Strange Monkey Business-like things in GBIF KOS Document
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
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
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
> NCBO FAQ:
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
> 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 , 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
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 :
More information about the tdwg-content