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Re: [Obo-discuss] New ontologies for systems biology
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From: Nicolas Le N. <le...@eb...> - 2011-06-23 15:50:54
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Dear OBO enthusiasts, It must be one of my most delayed answer ever, 3 years! KiSAO was indeed a bit thin at the time as Michael pointed out. Since then it evolved much. We refactored the ontology to separate the algorithms themselves from the their characteristics and the parameters needed to run instances of them. The ontology is developed in OWL2 but we provide an OBO export (no round-tripping however ...). You can fine more information at: http://biomodels.net/kisao/ KiSAO is used by the Simulation Experiment Description Markup Language, to specify the algorithm used during such an experiment. http://sed-ml.org/ In order to facilitate the use of the ontology, we provide a library in Java: http://biomodels.net/kisao/libkisao.html We would therefore like to resubmit KiSAO as "an OBO Foundry candidate ontology or other ontology of interest". Best regards, On 17/05/08 18:44, Michael Ashburner wrote: > 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 > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Obo-discuss mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-discuss -- Nicolas LE NOVERE, Computational Systems Neurobiology, EMBL-EBI, WTGC, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521 Fax:468, Skype:n.lenovere, AIM:nlenovere, twitter:@lenovere http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ |