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Dear List,

I'm happy to announce a new release of TEDDY! Besides a much clearer
top-level structure (1) and new reasoning capabilities (5) the most
important improvement is the completed (in terms of definitions)
Temporal Behaviour branch (2).

You can download the ontology at

http://teddyontology.svn.sourceforge.net/viewvc/teddyontology/teddy/tags/rel-2009-10-16/ontology/teddy.owl
http://teddyontology.svn.sourceforge.net/viewvc/teddyontology/teddy/tags/rel-2009-10-16/ontology/teddy-inferred.owl

(for the second version see (5) below).

The documentation (OWLDoc) is available online:

http://teddyontology.svn.sourceforge.net/viewvc/teddyontology/teddy/tags/rel-2009-10-16/doc/index.html

There you can look at all the classes and browse the subclass hierarchy...


The news in detail:

(1) New top-level structure

The main branching of TEDDY is now much more coherent and
clear. The long discussion about whether a Bifurcation is a
Behaviour or a Behaviour Characteristics was resolved by
introducing a fourth branch: "Behaviour Diversification". More
concrete names were assigned for the other branches. The new
top-level branching is as follows:

- Temporal Behaviour (concrete behaviours of a model, more or less
the same as trajectories): Oscillation, Steady State, Fixed
Point, Cycle, ...
- Behaviour Characteristic (properties to characterise concrete
behaviours): Period, Amplitude, ...
- Behaviour Diversification (system properties describing the
ability of systems to exhibit different behaviours) :
Bifurcation, Bi-Stability
- Functional Motif (structural features of a system necessary for
specific function): Negative Feedback, FFL, ...

(2) Temporal Behaviour branch finished

Each term in this branch now has a definition and a reference for
this definition. The structure of this branch was
renewed. Temporal Behaviours are now classified as Fixed Points,
Periodic
Orbits, and Non-Periodic Orbits. Beside this three subclasses of
Temporal Behaviour named classes are introduced, see (4). Many of
the Temporal Behaviours are characterised by new relations, see (3).

(3) New relations

Some new relations were introduced: hasStability, adjacentTo,
convergeTo. This relations are used to characterise Temporal
Behaviours. hasStability relates a Temporal Behaviour to Stability
(which is a Behaviour Characteristics), e.g.

Stable Node hasStability Stable.

The other two relations can describe the surrounding of a Temporal
Behaviour, e.g.

Center adjacentTo Non-Isolated Cycle.

This relations become important in the definition of named classes
and the automatic inference of their subclasses, see (4) and (5).

(4) Named classes

Beside the main hierarchy below Temporal Behaviour some named
classes were created to account for often used general terms,
e.g. Attractor. This classes don't have manually asserted
subclasses. Rather we use restrictions to characterise this
classes, e.g.

Attractor EquivalentTo hasStability some Attracting

, which states that all Temporal Behaviours having at least one
hasStability relation to Attracting are members of the class
Attractor. This restriction can be used to automatically infer
subclasses of the named classes, see (5).

(5) Reasoning capabilities -- inferred ontology

A reasoner can be used to infer the subclasses of the named
classes. For example Stable Fixed Point will inferred as a subclass
of Attractor. This means that not all subclass relations are
explicitly given in TEDDY, more precisely in "teddy.owl". The full
subclass hierarchy can be inferred by a reasoner (e.g. FaCT++ and
Pellet are bundled with Protege). Because not everybody will have
a reasoner at hand we also provide a version of TEDDY were all
inferred subclass relations are explicitly given:
"teddy-inferred.owl". This version is also used to generate the
OWLDoc documentation.

(6) Curve characteristics

There was a problem with some terms like "Strictly Monotonic
Behaviour": they are only applicable in one dimensional
systems. In fact the term "Strictly Monotonic" is more often used
to characterise the curve of a single variable rather than a
behaviour of a whole system. Therefore such terms were moved to
Curve Characteristic and adequately renamed.

(7) Obsolete terms: new conventions

All obsolete terms are now in a single branch "_obsolete", which
has the special ID " TEDDY_obsolete". The reason for making a term
obsolete is given in the Definition. The name of an obsolete term
is marked by "((obsolete))". All other annotations, relations and
restrictions of obsolete terms are deleted.



Hopefully, this new release will reactivate the discussion about
representing dynamic aspects of bio-models. Your remarks are welcome!


Regards,

Christian.


--
Christian Knuepfer
Friedrich-Schiller-Universitaet Jena
Institut fuer Informatik
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Phone: Intl.+49/3641/9-46353
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e-mail: mailto:christian.knuepfer@uni-jena.de
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