EBI Groups Computational Neurobiology TEDDY

Announcement of the release rel-2011-08-30

Announcement of the release `rel-2011-08-30`

We are please to announce a new release of the Terminology for the Description of Dynamics (TEDDY). The main changes are summarised below. You can explore the ontology via BioPortal.

You can post comments or questions on the discussion list. For term requests please use the term tracker.

News in TEDDY rel-2011-08-30

1. OWL Structure

1.1 TEDDY URL

The base URI was changed from http://biomodels.net/teddy/ to http://biomodels.net/teddy/TEDDY#

1.2 Obsoleteness

Obsolete classes were annotated as owl:deprecated.

1.3 Disjointness

Disjoint class axioms were added.

2. Annotations

2.1 TEDDY-specific annotations

teddy:DisplayName, teddy:Synonym, teddy:Reference and teddy:Definition were replaced with more common rdfs:label, skos:altLabel, rdfs:seeAlso and skos:definition.

2.2 Human-readable reference descriptions

Human-readable descriptions of the references were added as rdfs:comment annotations.

2.3 Language metadata

Language metadata (@en) was added to the rdfs:label, skos:altLabel and skos:definition annotations.

2.4 Synonym capitalization

Unnecessary synonym first letter capitalization was removed (see [2]).

2.5 Proper noun capitalization

Missed proper noun capitalization was added (see [2]).

2.6 Inter-TEDDY annotations

More inter-TEDDY annotations were added to the descriptions.

3. Content

3.1 Definitions and references

Most of the TEDDY terms were annotated with definitions and links to the resources describing them.

3.2 Hyperbolic equilibrium point vs saddle?

In TEDDY rel-2011-03-10 'saddle point' (and only it) was annotated with synonym 'hyperbolic fixed point'.
In TEDDY rel-2011-08-30 'hyperbolicity' property was introduced: 'A fixed point [TEDDY_0000086] is said to be hyperbolic if all eigenvalues of the Jacobian matrix have non-zero real parts. A limit cycle [TEDDY_0000051] is called hyperbolic if the fixed point of the Poincare map is hyperbolic', which is possesed by spirals, nodes and saddles.

3.3. Attractor / repellor vs stability

In TEDDY rel-2011-03-10 'liapunov stable behaviour' was an ancestor of 'asymptotically stable behaviour', 'attractor' was equal to 'stable behaviour' (not necessarily asymptotically); 'saddle' was not marked as unstable, none of 'stable node', 'stable spiral', center were children of the 'stable fixed point'.
In TEDDY rel-2011-08-30 the 'attractor' was defined as 'the limit set which corresponds to the particular type of stable solution and attracts phase trajectories from a sertan region of initial conditions', the equivalent axiom between 'stable behaviour' and 'attractor' was removed, a 'regular attractor' term was added ('asymptoticallly stable') add GCI axioms: 'fixed point/limit cycle, which is asymptotically stable => regular attractor' were added.

3.4 Heteroclinic path vs saddle connection

In TEDDY rel-2011-03-10 'heteroclinic / homoclinic orbit' were descendants of 'saddle connection' and described as 'A Saddle Connection connecting two different Saddle Points / a Saddle Point to itself'.
In TEDDY rel-2011-08-30 according to [1] these terms were split into 'heteroclinic / homoclinic orbit' (not a child of a saddle connection) and 'heteroclinic / homoclinic saddle connection' (child of both).

3.5 Behaviours, system and attractors

In TEDDY rel-2011-03-10 'bistable behaviour' was annotated as 'a perturbation behaviour shown by a system with two different attractors. Depending on the initial state the system tend to the one or the other attractor' and the axiom 'bistable bahaviour hasPart exactly 2 attractors' held.
In TEDDY rel-2011-08-30 this axiom was replaced with GCI: (system that) hasPart exactly 2 attractor SubClassOf hasFeature some 'bistable perturbation behaviour'

3.6 Bifurcation and fixed points

In TEDDY rel-2011-03-10: 'Hopf bifurcation' hasSuperPart some 'unstable spiral'; 'hasSubPart some 'stable spiral'
In TEDDY rel-2011-08-30: 'Hopf bifurcation' destroys some 'unstable spiral'; creates some 'stable spiral'

3.7 Zero growth vs unbounded growth

In TEDDY rel-2011-03-10: zero growth was a descendant of unbounded growth: zero growth is_a linear growth is_a polynomial growth is_a unbounded growth is_a growth.
In TEDDY rel-2011-08-30: unbounded growth term was removed from this hierarchy chain.

Announcement of the release rel-2011-08-30