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

Shawn Bowers bowers at gonzaga.edu
Fri Feb 18 06:46:52 CET 2011

Hi Hilmar,

>> 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).

There are two ways to type things in OWL, classes and properties (I
should have said properties in addition to classes above, since OBOE
also introduces properties). So, in this way, the "inheres_in"
property is how EQ prescribes type information on "instances". It also
sounds like it prescribes E's and Q's (since this really defines what
inheres_in is), and so at least implicitly these are types also
"introduced" by EQ.

> 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.

But, one would imagine that designating a class within an inheres_in
statement (even if anonymous) means it is either an E or a Q (at least
implicitly, i.e., it may not be inferable from EQ that this is the
case, but that seems like a detail). Of course, PATO as a realization
of EQ uses a Quality class.

> 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.

Yes, this is true.

BTW. I'm a bit confused though -- is EQ an OWL ontology? Or is it
purely an abstract model that prescribes a convention for defining
qualities, with concrete quality and entity ontologies being drawn
from other places (like PATO)? Where is the inheres_in property

> 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".

I agree with this.

As an example, one of the driving use cases for OBOE is annotating
relational data sets in which the attributes within a given data set
is tagged with observation/measurement types and from these
annotations OBOE instance data (i.e., sets of triples) are
automatically generated.

> 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.

Right ... and I think ideally EQ models could be used within OBOE for
assigning qualities to specific observations. This would allow for
both the reasoning abilities of OBOE (e.g., context, units, etc.) plus
those for qualities via EQ.


> On Thu, Feb 17, 2011 at 11:28 AM, joel sachs <jsachs at csee.umbc.edu> wrote:
>> 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: 128-139.
> http://psb.stanford.edu/psb-online/proceedings/psb06/good.pdf
>        -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================

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