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From: Nicolas Le novère <lenov@eb...>  20080519 22:16:37

Barry Smith wrote: Barry, Thanks a lot for your comments. > mixing of singular and plural nouns (Gillespie's direct method is_a > nonspatial Gillespielike methods) That's a bug, to be corrected. > use of acronyms That should be homogeneised indeed. Although I am not sure in which direction :) For instance the Livermore solver branch would gain a lot in clarity if we were to systematically use the acronyms as the official names... > use of relations (hasproperty) not in RO That one is the tricky one. Canwe proposed new relationships to OBO RO? The problem I see is that RO is mainly geared toward relationships between biological entities. This is why we gave up using it for the RDF encoding of MIRIAM annotations for instance (see http://www.ebi.ac.uk/compneursrv/miriammain/mdb?section=qualifiers) Must all the relationship of OBO belong to RO? To be discuss in July I guess. > inconsistent use of 'type' (continuous variable is_a type of variable > is_a spatial resolution characteristic) Bug. To be corrected.  Nicolas LE NOVERE, Computational Neurobiology, EMBLEBI, WellcomeTrust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074 Skype:n.lenovere http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nlenovere@... 
From: SusannaA Sansone <sansone@eb...>  20080519 21:12:18

> Also some of this ground is being covered by OBI > Data Transformation Branch. Is Nicolas working with the OBI people? Not yet, Barry. Nicolas if you are interested we are happy to help. Susanna Barry Smith wrote: >There are also other problems, for instance > >mixing of singular and plural nouns (Gillespie's >direct method is_a nonspatial Gillespielike methods) >use of acronyms >use of relations (hasproperty) not in RO >inconsistent use of 'type' (continuous variable >is_a type of variable is_a spatial resolution characteristic) > >Also some of this ground is being covered by OBI >Data Transformation Branch. Is Nicolas working with the OBI people? >BS > > >At 09:44 AM 5/17/2008, 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 ? >>> >>>Objectmodel SBML MIASEML ? (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/compneursrv/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@... >>>rostock.de) >>> >>>The TErminology for the Description of DYnamics >>>=============================================== >>>http://www.ebi.ac.uk/compneursrv/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 "steadystate". More complex can be >>>"heteroclinic orbit" or "halfstable asymptotic behaviour". >>> >>>Characteristics are the quantitative properties that characterise >>>behaviours. For instance a periodic oscillation is characterised by >>>a "period", a steadystate 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 (tral@...) >>> >>>Best regards, >>> >>> >>>Nicolas LE NOVERE, Computational Neurobiology, EMBLEBI, Wellcome >>>Trust >>>Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel: >>>+441223494521 >>>Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere@... >>>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 >>>_______________________________________________ >>>Obodiscuss mailing list >>>Obodiscuss@... >>>https://lists.sourceforge.net/lists/listinfo/obodiscuss >>> >>> >> >>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/ >>_______________________________________________ >>Obodiscuss mailing list >>Obodiscuss@... >>https://lists.sourceforge.net/lists/listinfo/obodiscuss >> >> > > > > >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/ >_______________________________________________ >Obodiscuss mailing list >Obodiscuss@... >https://lists.sourceforge.net/lists/listinfo/obodiscuss > > 
From: Barry Smith <phismith@bu...>  20080519 19:50:27

There are also other problems, for instance mixing of singular and plural nouns (Gillespie's direct method is_a nonspatial Gillespielike methods) use of acronyms use of relations (hasproperty) not in RO inconsistent use of 'type' (continuous variable is_a type of variable is_a spatial resolution characteristic) Also some of this ground is being covered by OBI Data Transformation Branch. Is Nicolas working with the OBI people? BS At 09:44 AM 5/17/2008, 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 ? > > > > Objectmodel SBML MIASEML ? (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/compneursrv/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@... > > rostock.de) > > > > The TErminology for the Description of DYnamics > > =============================================== > > http://www.ebi.ac.uk/compneursrv/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 steadystate. More complex can be > > heteroclinic orbit or halfstable asymptotic behaviour. > > > > Characteristics are the quantitative properties that characterise > > behaviours. For instance a periodic oscillation is characterised by > > a period, a steadystate 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 (tral@...) > > > > Best regards, > > > >  > > Nicolas LE NOVERE, Computational Neurobiology, EMBLEBI, Wellcome > > Trust > > Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel: > > +441223494521 > > Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere@... > > 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 > > _______________________________________________ > > Obodiscuss mailing list > > Obodiscuss@... > > https://lists.sourceforge.net/lists/listinfo/obodiscuss > > > >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/ >_______________________________________________ >Obodiscuss mailing list >Obodiscuss@... >https://lists.sourceforge.net/lists/listinfo/obodiscuss 
From: Michael Ashburner <ma11@ge...>  20080519 08:21:32

THAT looks better ! I must have had some funny filter set on by OBO Edit. Michael On 17 May 2008, at 19:00, Nicolas Le novère wrote: > 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. > > Mike, > > I do not understand your comment. Attached is a screenshot of what > you should see. Only two terms are children of the root, and they > certainly have children. Couldit be due to a different version of > OBOedit? I used 1.002. > >> Will TeDDy be available as an OBO format file? > > I am not sure about that. The current version could actually be > encoded in OBO, but not what we have in mind for the fully > developed ontology. Indeed, we will need to include constraints, > such as sequentiality (a behaviour X is formed by a repetition of a > behaviour Y followed by a behaviour Z), or conditionality > (piecewise inheritance) etc. That may prove to be a challenge. > >> 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 ? >>> >>> Objectmodel SBML MIASEML ? (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/compneursrv/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@... rostock.de) >>> >>> The TErminology for the Description of DYnamics >>> =============================================== >>> http://www.ebi.ac.uk/compneursrv/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 “steadystate”. >>> More complex can be “heteroclinic orbit” or “halfstable >>> asymptotic behaviour”. >>> >>> Characteristics are the quantitative properties that >>> characterise behaviours. For instance a periodic oscillation is >>> characterised by a “period”, a steadystate 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 (tral@...) >>> >>> Best regards, >>> >>>  >>> Nicolas LE NOVERE, Computational Neurobiology, EMBLEBI, >>> Wellcome Trust >>> Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel: >>> +441223494521 >>> Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nlenovere@... >>> 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 >>> _______________________________________________ >>> Obodiscuss mailing list >>> Obodiscuss@... >>> https://lists.sourceforge.net/lists/listinfo/obodiscuss >>  >>  >> 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/ >> _______________________________________________ >> Obodiscuss mailing list >> Obodiscuss@... >> https://lists.sourceforge.net/lists/listinfo/obodiscuss > > >  > Nicolas LE NOVERE, Computational Neurobiology, > EMBLEBI, WellcomeTrust Genome Campus, Hinxton, Cambridge, CB10 > 1SD, UK > Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074 > Skype:n.lenovere > http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: > nlenovere@...<kisao.png> >  > 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/ > _______________________________________________ > Obodiscuss mailing list > Obodiscuss@... > https://lists.sourceforge.net/lists/listinfo/obodiscuss 