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

Steve Baskauf steve.baskauf at vanderbilt.edu
Fri Feb 18 16:26:19 CET 2011

Might I make a suggestion?  When the topic of a thread diverges 
significantly from the original subject line, let's send it to the list 
with a new subject line that reflects the nature of the new thread.  I 
don't know if I'm the only person who does this, but I do go to the list 
archives to try to find old posts that I remember and to which I would 
like to refer.  However, that gets really hard when there are a lot of 
posts and the subject lines don't correspond to the topic of the posts.  
This is a good example of a series of posts to which I'm likely to want 
to refer in the future but I have a feeling I wouldn't find them under 
this subject line.


Shawn Bowers wrote:
> 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.
> Right.
>> 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
> defined?
>> 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.
> Shawn
>> 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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Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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