From: Michael A. <ma...@ge...> - 2008-05-17 17:44:46
|
Nicolas - did anyone get nak to you on this ? I have no objections to them being added to OBO, but others should chime in. I must say that KiSAO looks a bit thin, in that many of the terms are direct off the root and without child terms. Will TeDDy be available as an OBO format file? Michael Michael On 6 May 2008, at 09:50, Nicolas Le Novere wrote: > Dear OBOers, > > OBO currently propose the Systems Biology Ontology (SBO). This > ontology has been developed to add a semantic layer to quantitative > models used in systems biology. Initially planned to allow > conversion between different modeling framework, it has been > extended to provide an interface between different representations > such as mathematical (SBML), biochemical (BioPAX) or graphical > (SBGN). SBO has now left prototyping phase and is a recognized > resource in the CSB field. But SBO is not sufficient. It only deals > with models. However, the "modeling" process involves model design > (biological and mathematical) but also simulation and analysis of > the results (plus comparison with experimental recording). This is > why we need other ontologies corresponding to the other steps. Here > is the matrix of "standards" we aim to: > > > model simulation numerical result > > Checklist MIRIAM MIASE ? > > Object-model SBML MIASE-ML ? (but some > efforts started) > > Ontology SBO KiSAO TeDDy > > > I would like to register KiSAO and TeDDy to OBO: > > The Kinetic Simulation Algorithm Ontology (KiSAO) > ================================================= > http://www.ebi.ac.uk/compneur-srv/miase/kisao.html > > KiSAO classifies the algorithms by different characteristics and > puts them into relation. Model characteristics include the type of > variable that are used for the simulation – an indication for how > the model can be simulated (discrete or continuous), and > information on the spatial resolution. Numerical kinetic > characteristics include the system's behaviour (deterministic or > stochastic) as well as the distinction between fixed and adaptive > timesteps. > > Characteristics relate to each other by OBO is a relationships, as > do concrete algorithms to each other. For instance, the class > discrete variable (A) is a subclass of the class type of variable > used (B). Because is a is transitive, discrete variable is also a > model characteristic. Concrete algorithms are related to > characteristics by a KiSAO specific relationships HasProperty. A > simulation algorithm A hasProperty P if, and only if, for any > simulation algorithm a, a being an instance of A, it exists a > property p, where p is an instance of P. For example, Gillespie's > direct method (A) has the property adaptive timestep (P). Using > this structure, all algorithms will appear on more than one leaf of > the ontology tree. If completely characterised, each algorithm will > occur on four leaves. > > In addition to its identifier and name, a KiSAO term contains a > definition, which is the reference to the publication in which the > algorithm has been published, a list of relationships, and > optionally a brief description, bibliography identifiers and synonyms. > It has been recently decided that the KiSAO terms associated with > algorithms would carry a list of mandatory parameters required for > applying those algorithms. This has not been yet implemented, but > should be soon. > > KiSAO is developed with OBOedit and available in OBO flat format. > The main developer of KiSAO is Dagmar Koehn (dk103@informatik.uni- > rostock.de) > > The TErminology for the Description of DYnamics > =============================================== > http://www.ebi.ac.uk/compneur-srv/teddy/index.html > > TeDDy is an ontology for encoding dynamical behaviour and allow > their comparison. It will provide a mean to answer questions such > as: “How do I find a model describing the protein X and displaying > a periodic oscillation?”, “What behavioural features do all these > models have in common?”, “Which model displays a behaviour matching > my experimental data?” > > TeDDy contains three branches which are linked through a variety of > relationships. Within a branch, the terms are linked by OBO is a > relationships. > > Behaviours classify the way a dynamical system changes with respect > to some aspect of the environment (note that a system here can be a > variable, a subset of the model's variables or the complete model). > Simple examples are “cycle”, or “steady-state”. More complex can be > “heteroclinic orbit” or “half-stable asymptotic behaviour”. > > Characteristics are the quantitative properties that characterise > behaviours. For instance a periodic oscillation is characterised by > a “period”, a steady-state by a “limit” etc. > > Functionalities describe the functional motifs of a submodel, such > as “negative feedback” or “switch”. > > TeDDy is developed with Protege and available in OWL. The main > developer of TeDDy is Christian Knuepfer (tr...@mi...) > > Best regards, > > -- > Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome- > Trust > Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel: > +441223494521 > Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho... > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save > $100. > Use priority code J8TL2D2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http:// > java.sun.com/javaone > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss |