Hi, First off ... "Horray for the demise of the reaction element". From your description, the script of Andrew's pulls apart the components and adds in the formerly implicit rate*stoichiometry as I would expect, though I would like stoichiometry to be represented as an explicit variable so we can refer to it and not have to infer from constants in the math. There may be some argument to more decomposition of this into separate components, but that is work in progress for Best Practices and Sarala's annotation work.
As for keeping some sane biology in the models that is lost by removing reactions. Yes, Sarala's work will end up being the practice we want to take for this, but at the moment it is not proven and considering this is a public resource lets stick to something already specified for cellml metadata which in time can be automatically migrated to (or simply complimented with) something in Sarala's domain. Briefly, Biopax addresses the role of an entity by way of its place in an interaction process, whereas our reaction elements were quite explicit about a role. I would propose something very simple. Use the biological entity metadata (see section 4.10 Biological Entity of http://www.cellml.org/specifications/metadata/cellml_metadata_1.0#sec_general_metadata) to refer to a prescribed role within our own controlled vocab that is designed only for the purpose of maintaining this role data. The <cmeta:bio_entity> can contain a collection of references which allow for general concepts to be mapped to a CellML element as well as a specific physical entity from say a protein database. This means that each variable that had a role in the reaction element would now need a cmeta id assigned to it and the respective rdf written out for the bioentity data. The <rdf:value> of the identifier would be the URI of the respective role in the role vocab. It would make sense(and help the migration/complement of Srala's work) if the roles for modulators could follow those set out in biopax (see pages 17-19 of http://www.biopax.org/release/biopax-level2-documentation.pdf). So we would end up with simple URIs such as the following (which map into terms within some ontological context in the imaginary document http://cellml.org/vocabularies/2007/05/17/reactionmapping): For the role of entities http://cellml.org/vocabularies/2007/05/17/reactionmapping#reactant http://cellml.org/vocabularies/2007/05/17/reactionmapping#product http://cellml.org/vocabularies/2007/05/17/reactionmapping#catalyst For the kinds of modulators http://cellml.org/vocabularies/2007/05/17/reactionmapping#activation http://cellml.org/vocabularies/2007/05/17/reactionmapping#inhibition http://cellml.org/vocabularies/2007/05/17/reactionmapping#inhibition-allosteric http://cellml.org/vocabularies/2007/05/17/reactionmapping#inhibition-competitive http://cellml.org/vocabularies/2007/05/17/reactionmapping#inhibition-irreversable http://cellml.org/vocabularies/2007/05/17/reactionmapping#inhibition-noncompetitive http://cellml.org/vocabularies/2007/05/17/reactionmapping#inhibition-other http://cellml.org/vocabularies/2007/05/17/reactionmapping#inhibition-uncompetitive http://cellml.org/vocabularies/2007/05/17/reactionmapping#activation-nonallosteric http://cellml.org/vocabularies/2007/05/17/reactionmapping#activation-allosteric Sarala has a rule for generating the cmeta ids of variables and math, so perhaps it is best to make up an xslt that takes a cellml model and generates the cmeta ids for the elements and puts them back in to the elements and perhaps even creates stub rdf description elements for each of them. If you send me a component that has been decomposed from a reaction element using Andrew's script, then I'll add in the rdf metadata in the way I was thinking and post it back here. cheers Matt On 5/17/07, James Lawson <[EMAIL PROTECTED]> wrote: > Dear All, > > This email is aimed at anyone who has comments, but we particularly want > to draw Matt's attention. > > In the CellML meeting yesterday I brought up the issue of replacement of > reaction components with straight math. At present PCEnv isn't handling > reaction components well - models which use reaction components aren't > integrating, for one. There are also issues with math elements not being > picked up if they are under role elements. Andrew has written a script > to pull these math elements up a level so that they're a direct child of > the component, not the role element. The script also defines delta > variables as rate * stoichiometry. Running this script on the models > which contain reaction components has cleared up most of the errors with > undefined delta variables, so now many of the models with reaction > components can now be loaded in PCEnv. The problem is that *none of > them* will integrate properly. I am making the assumption that this > effect is due to the reaction component, not the models, since it is so > widespread among many very different models. > > I'm going to start rebuilding models without reaction components. > However, one of the primary issues around this is that the information > represented by the attributes defined in the reaction components is, > while not essential for computation of the model, definitely something > that we want to keep. For example, what species are reactants, products, > catalysts, activators, inhibitors (and what kind of inhibitor,) etc. > Ideally, these attributes would be recorded as metadata. We don't as yet > have this facility, however. > > So the questions are: > 1.) what to do with this data meanwhile > 2.) how to redesign reaction descriptions using a combination of math > and metadata. > > One of the reasons we're seeking your input Matt, is that ontologies > such as BioPAX could be really useful in providing a framework for how > we assign metadata to reactions, in a biological sense. Also, Sarala > mentioned in the meeting yesterday that she was using BioPAX to describe > reactions in her work. > > Regarding the first question, some of the ideas that were suggested were: > a.) use commenting to describe the attributes of each reaction > b.) keep the files (well, we already do anyway,) that describe the > models in terms of reaction components and refer back to them later when > we have the facilities to enter metadata on reactions to the models > which have been rebuilt without the reaction components. > > So if anyone has any comments on this, they'd be much appreciated. > > James > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > _______________________________________________ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
