> If you could actually translate some of the fundamental concepts of your > work I think that would be very useful.
agreed! I'm sure people on this list won't mind too much if the english is not perfect :) Andre. > > Kind regards, > James > > Ely Edison Matos wrote: >> Hello all, >> James, my Msc. dissertation, recently concluded, was about the use of >> ontologies to enrich semantically the CellML Models. I've proposed a >> initial ontology represented in OWL-DL and using SWRL, called CelO >> (Cell Component Ontology) with 3 "sub-ontologies": one to represent SI >> units and quantities, other to represent the biological domain terms >> and another to represent the model. >> >> My proposal was exactly to have "atomic components" (models with a >> single component or, at least, a single "interface" - when a component >> "encapsules" other components and only it is visible to external >> world). Each "atomic model" owns a interface (input/output variables) >> semantically annoted to let one to make "semantic queries" about >> models (using SPARQL). This let me to do questions as "which are the >> components related with SodiumIonChannel?", taked in account that this >> "knowledge" is extracted from the names of variables in CellML Model >> (like "I_Na") and some inferences (like "I" is the symbol of "ampere" >> that measures "eletric_current", then this variable is associated with >> eletric_current; as it is defined inside the component "mebrane" and >> "Na" is the symbol of "Sodium", it can be associated with >> .SodiumIonChannel). This is a very simple example. >> . >> Each "CelO Model" has a reference to the correspondent CellML Model, >> to let compose "atomic components" and create a "composed model", with >> components of diverse models (as a rough example, a SodiumChannel of >> Hodking_Huxley inside a Noble model). The CelO Models are stored in a >> relational database and inference engines can be used to do queries. >> >> I've implemented a "framework" (as web service) that offers all this >> services (registry, query, "execute", compose models). >> >> This work is very incipient, given my "almost null" knowlegde about >> intrinsics of biological domain. As my Master Program is about >> Computational Modeling, my focus was strongly directed to the >> "modelling" part, not the "biological" part. My objective was provide >> a "high level" view of CellML Models. >> >> Unfortunately my dissertation is written only in brazilian portuguese. >> I've submmited some papers but I didn't get success. However, if there >> is some curiosity I can try to translate the main ideas. >> >> Sorry by intromission and the bad english, >> >> Ely Matos >> Computational Modeling Master Program >> UFJF/Brazil >> >> >> ----- Original Message ----- From: "James Lawson" >> <[EMAIL PROTECTED]> >> To: "CellML Discussion List" <cellml-discussion@cellml.org> >> Sent: Wednesday, April 30, 2008 11:04 PM >> Subject: Re: [cellml-discussion] Suggestions regarding search and >> browse utility for CellML Repository >> >> >> >>> Hi Abhishek, >>> >>> Good to hear from you, you make some very good points. I apologise if >>> someone has already raised these points, I've just come back after being >>> away for a couple of weeks and I'm going through my many unanswered >>> emails. >>> >>> So at the moment, one of the things I am thinking a lot about is >>> ontological annotation of CellML models. I've just been to visit Neil >>> Wipat's lab at the University of Newcastle, and I talked quite a lot >>> with him and members of his group about ontologies and how they might be >>> of use to the CellML community. So one of the things that the new CellML >>> repository will handle much better than the current one is the manner in >>> which a user can view models and their interrelationships, whether these >>> are based directly on CellML relationships such as import based >>> modularity or whether they are based on relationships inferred from >>> ontological tags. >>> >>> I'll definitely have a look at MeSH - what we're planning to do (I >>> believe) is let the CellML-Bio Ontology import as much as possible from >>> other ontologies, and let Sarala's ontological framework stand as our >>> contribution. Where we conclude that there is no ontology that covers >>> what we are trying to do in a satisfactory manner, we'll create our own. >>> I can see this happening in the area of synthetic biology, which is only >>> just starting to be represented by formats like CellML and SBML. So a >>> tree-like browsing structure as constructed from MeSH tags or similar >>> could be one of a number of different ways of viewing the models. You >>> could also do searching by terms, or construct trees according to terms. >>> For example, you could have 'species' as the top level and 'organ' as a >>> lower level, and 'cell type' as the bottom. So then you'd get a tree >>> sorted first by species, then by organ type, say heart, pancreas, liver, >>> etc. and then by cell type, so within the heart: myocardium, epicardium, >>> etc. etc. >>> >>> The possibilities for how we display fully tagged models are huge, so we >>> do need to form some kind of system of constraints - or at least provide >>> a set of default viewing architectures based on what workflows we >>> anticipate for users. >>> >>> When we decompose models into modular elements, this kind of tagging is >>> going to be absolutely crucial for model reusability and for the process >>> of figuring out what module you want and where to get it. >>> >>> As far as the technology for web services and programmatic access to the >>> repository database, that isn't something we've thought about much until >>> now, but on our travels Mike and I have realised that this is really >>> quite important. In fact, it was often one of the first questions I was >>> asked when I was discussing the CellML repository. A lot of people are >>> seeing the repository not simply as a database containing individual >>> models, but as an dataset in and of itself. We need to work on this - >>> I'm told Mike mentioned it at the Auckland CellML meeting last week. >>> >>> Hope you found this of some interest, >>> James >>> >>> Abhishek Tiwari wrote: >>> >>>> As growing no of models in CellML repository I feel that CellML >>>> Repository can be made more user friendly by implementing one or more >>>> suggestions mentioned below- >>>> 1. A Tree like browsing mechanism in which end child node of tree will >>>> have model. For that we need to have classification system for the >>>> models based on Physiological system or better say using MeSH (Medical >>>> Subject Headings,something like >>>> http://www.nlm.nih.gov/cgi/mesh/2008/MB_cgi). Models can be in multiple >>>> classes and basically model metadata can have details for the >>>> classification purpose like keywords. Domain ontologies can be used to >>>> give better description for tree like representation. >>>> 2. For a given model at the end of overview similar models (basic or >>>> improved models or more complex models) can be reported (Similar to >>>> model variants). >>>> 3. Web services to search and download CellMl models for non ABI >>>> tools ( >>>> using CellMl API or Web API for CellMl). >>>> >>>> I don't know if efforts to handle above is under development or already >>>> exists so I thought to write you all. >>>> >>>> abhishek >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >> >> _______________________________________________ >> 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 -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] _______________________________________________ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
